Ligands are typically. Medical search. Frequent questions

While these molecules typically have trigonal planar geometry, when bonded to a metal center, they become tetrahedral. (wikipedia.org)
In addition to the simple Lewis acids, there are several complex molecules that can act as both L- and Z-ligands. (wikipedia.org)
These are referred to donor buttresses, and are typically formed when large boron-alkyl molecules complex with a metal center. (wikipedia.org)
Transition metals are likely to form compounds in which they are centrally bonded to several molecules or ions, known as ligands. (wolfram.com)
Virtual screening software platform, Blaze™ uses the 3D electrostatics and shape of a defined ligand to rapidly search large chemical collections for molecules with similar properties. (cresset-group.com)
Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1. (rcsb.org)
A synthetic, specially- designed oligonucleotide with the ability to recognize and bind a protein ligand molecule or molecules with high affinity and specificity. (genomicglossaries.com)
This is typically achieved through post-synthetic functionalization by anchoring molecules on the surface of an exfoliated 2D crystal, but it inevitably alters the long-range structural order of the material. (tudelft.nl)
Inorganic chemistry encompasses the compounds - both molecular and extended solids - of everything else in the periodic table , and overlaps with organic chemistry in the area of organometallic chemistry, in which metals are bonded to carbon-containing ligands and molecules. (wikibooks.org)
Metal nanoparticles are typically covered with organic molecules called ligands, which generally prevent the formation of metal-metal bonds between particles. (scitechdaily.com)
Typically, protein or peptide dynamics take place at longer timescales, while the timescales of water dynamics are around picoseconds, mainly due to the high mobility of water molecules and frequent changes in the hydrogen bonding state. (fu-berlin.de)
Ligand-based drug designers utilize Flare to closely examine, compare, and prioritize their molecules, based on their shape, electrostatics, and binding activity. (cresset-group.com)

CD137 ligand (CD137L) is a type II membrane protein and part of the TNF superfamily. (fishersci.com)
The present study used in vitro expression systems to investigate interactions of members of the KDN series with δ-κ heterodimers through competition binding using selective ligands and the mitogen-activated protein kinase (MAPK) assay. (aspetjournals.org)
G-protein-coupled receptors (GPCRs) are typically considered to function as monomers. (aspetjournals.org)
If it's a ligand and protein atom, there may be a deficiency in the scoring of ligand-protein repulsive. (rosettacommons.org)
I have not found that there have been any instances of the ligand forming a bond with the protein. (rosettacommons.org)
2.There is a known phenomenon, called "induced fit", whereby a target protein undergoes conformational changes upon ligand binding. (cecam.org)
The protein is typically found in the cytoplasm until it binds a ligand, which induces transport into the nucleus. (thermofisher.com)
Protein A affinity purification is the accepted industry standard for purifying monoclonal antibodies, yet multiple problems (link is external) present with industry use of this affinity ligand. (avacta.com)
The exorbitant costs of protein A affinity resins on an industrial scale mean that biomanufacturers typically use multiple cycles of affinity purification per batch of product, to allow for the use of smaller protein A affinity purification columns thus keeping cost down. (avacta.com)
The software enables them to closely inspect the detail of their ligand-protein complexes, using a variety of methods to gain useful insights into their protein targets and ligand series. (cresset-group.com)
With a variety of methods including docking and scoring, Electrostatic Complementarity™, molecular dynamics, pocket analysis, and water analysis (GIST and 3D-RISM), structure-based drug designers can gain new insights into protein-ligand binding. (cresset-group.com)
Based on established, proprietary methods around ligand and protein electrostatics, combined with the best of our own internal and open-source research, users are able to fully understand the features and interactions of their target structures. (cresset-group.com)
To support us with a membrane protein drug discovery project, we used the ligand- and structure-based components of Cresset's Flare™ platform. (cresset-group.com)
When a ligand attaches (binds), the KIT or PDGFRA receptor protein is turned on (activated), which leads to activation of a series of proteins in multiple signaling pathways. (medlineplus.gov)

Such drugs are devoid of the undesired central side effects that are typically mediated by the CB1 receptor. (nih.gov)
Studies show that necrotic death is induced by a ligand binding to a receptor, such as when apoptosis is initiated. (news-medical.net)
Typically, heterodimerization with ErbB2 forms the high affinity receptor complex. (rndsystems.com)
Gastrointestinal stromal tumor (GIST) is the most common human sarcoma and is typically driven by a single mutation in the Kit receptor. (aacrjournals.org)
The natural ligand for the Kit receptor is Kit Ligand (KitL), which exists in both soluble and membrane-bound forms. (aacrjournals.org)
If a drug molecule or a ligand is a message, an inbox is typically a receptor in the cell membrane. (sciencedaily.com)
This specificity of its binding and receptor activation mode makes it a suitable candidate for potential small-molecule-based drugs for class B1 GPCRs, like PTH1R, which currently lack oral administrative drug ligands. (sciencedaily.com)
Studies have shown that glucocorticoid receptor (GR) must be associated with a complex of chaperone proteins for ligand activation. (thermofisher.com)
In this review, we focused on studies addressing modulation of epigenetic mechanisms involved in NK cell-mediated responses, including both the epigenetic modulation of tumor cell NK ligand expression and NK cell receptor expression and function in different tumor models, highlighting studies in PCa. (bvsalud.org)
Receptor proteins have specific sites into which certain other proteins, called ligands, fit like keys into locks. (medlineplus.gov)

Over the last decade, significant progress has been made in this area, especially via the incorporation of Lewis acid moieties into multidentate, ambiphilic ligands. (wikipedia.org)
(B) Schematic representation of ambiphilic ligands. (frontiersin.org)
When ambiphilic ligands are used, the metal center coordinates to the L-type moiety of the ligand and the degree of coordination to the Lewis acid moiety is increased ( Figure 1B ). (frontiersin.org)

Affected individuals with no family history of GIST typically have only one tumor (called a sporadic GIST). (medlineplus.gov)
Furthermore, immunotherapy has revolutionized the management of melanoma, specifically, with inhibition of cytotoxic T-lymphocyte antigen-4 (CTLA-4), programmed death-1 (PD-1), which is expressed on lymphocytes, and programmed death ligand-1, which is expressed on tumor cells. (medscape.com)

The understanding of the nature and influence of metal→Z-ligand interactions has considerably improved and the scope of Lewis acids susceptible to behave as σ-acceptor ligands has been significantly extended. (wikipedia.org)
Docking results showed interaction between the proteins individually into selected ligands, except for gelsemine and vitamin E no interactions were shown. (ijpsonline.com)
Parkin, 2007 ) to define 2-center metal-ligand interactions of organometallic compounds as ML l X x Z z , where the ligand atoms are classified as L, X, and Z ligands ( Figure 1A ). (frontiersin.org)
Organometallic chemists have recognized how this basicity can be used to promote interactions between a TM and a Lewis acid moiety, where the acid acts as a σ-acceptor (L-type) and not a σ-donor (Z-type) ligand. (frontiersin.org)
Surprisingly, none of these reports have mentioned carbocations as Lewis acid Z-type ligands, and they neglect to examine the interactions between transition metals and persistent carbocations. (frontiersin.org)
The stimulus-sensor interactions typically regulate cellular functions to adapt to an abnormal environment, for example the diabetic condition. (lu.se)
1998). In both examples, the high affinity ligands can compete with the intramolecular interactions and release the catalytic domains for their in vivo targets. (lu.se)

Monomeric ErbB4 binds its ligands with low affinity. (rndsystems.com)

Upon binding, proteins and small-molecule ligands can undergo significant conformational changes, as schematized by the "induced fit" and "conformational selection" paradigms [1]. (cecam.org)

Owing to the vacant orbital present in Z-ligands, many have incomplete octets which allow them to readily accept a pair of electrons from other atoms. (wikipedia.org)
Many of the simplest Z-ligands are simple Lewis acids with electron-deficient center atoms such as BX3, BH3, BR3, AlX3, etc. (wikipedia.org)
However, the ligand itself is modified to display extra bonds between some atoms that were not in the input/native pdb files. (rosettacommons.org)
On the other hand, if it's an extra bond between two atoms of the ligand, the most likely cause is a bad rotamer. (rosettacommons.org)
I had a look at my files and it is definitely an issue of atoms in the ligand having bonds between them that shouldnt be there. (rosettacommons.org)

As the electrons are being donated from the central metal atom to the Z-ligand, the L-ligand donates its pair of electrons to the metal atom. (wikipedia.org)
Z-type ligands are Lewis acids that accept a pair of electrons from the metal to form a dative M ← Z bond (e.g. (frontiersin.org)

Similarly, repeated exposure to the harsh chemical conditions of elution and column cleaning procedures results in degradation and leaching of the affinity ligands, reducing column capacity and stunting optimal process performance. (avacta.com)
For the affinity purification of non-antibody products, affinity ligands (link is external) are lacking. (avacta.com)
Taken together with their high production costs we can see that antibodies are less than ideal ligands for affinity purification processes. (avacta.com)
The need to engineer new affinity ligands for use in affinity purification protocols rather than depending upon natural affinity ligands is clear. (avacta.com)
Engineered affinity ligands have the potential to isolate higher capacities of a wider variety of targets with the ability to calibrate the target affinity to the required application, allowing vital process innovation. (avacta.com)

In covalent bond classification, a Z-type ligand refers to a ligand that accepts two electrons from the metal center. (wikipedia.org)

The "death receptors", which typically cause cell death by apoptosis, can be activated by ligands, such as TNF. (news-medical.net)
Typically, phagocytosis is initiated when receptors on the immune cell surface bind to ligands which have coated a pathogen particle. (biophysics.org)

This unique type of bonding existing between two different ligands and the metal atom renders the complexes stable when present with a strong sigma donor ligand. (wikipedia.org)
In addition, for the metal base-stabilized borane complexes, the L-ligand that donates to the metal center plays an important role in the metal-boron bond length. (wikipedia.org)
Docking algorithms must therefore account for flexibility in order to allow predicting the structure of native complexes, but due to the computational cost typically only a limited flexibility is included [2,3]. (cecam.org)
The structures, properties, and reactivities of organometallic complexes depend mostly on their ligand environment. (frontiersin.org)

How the binding of small ligands like drugs affects the interaction patterns and thus the function of large macromolecular aggregates? (cecam.org)

The electrons donated from the L-ligand stabilize the Lewis acid into a tetrahedral form. (wikipedia.org)
The presence of Cp and CO ligands further stabilize the Fe-BPh3 bond. (wikipedia.org)
The Z-type ligand can stabilize a vacant orbital of the transition metal center while drawing electron density from the filled d-orbitals because of its σ-accepting properties. (frontiersin.org)

Thus, the conformational dynamics of proteins, water fluctuations, and their coupling play a crucial role in many biological functions, such as ligand binding. (fu-berlin.de)
Mutations in the KIT and PDGFRA genes lead to proteins that no longer require ligand binding to be activated. (medlineplus.gov)

1993). Based on these results, together with structural analyses of different ligand-binding models, it is apparent that SH2 domains bind distinct but overlapping sequence motifs. (lu.se)

Since transition metals (TMs) are typically defined as electron-deficient species, the majority of ligands that have been developed are electron-rich Lewis-basic moieties (L- and X-types) that aim to complete the valence shell of the transition metal (also known as the 18 electron rule). (frontiersin.org)

During recent years, the biotic ligand model (BLM) has been proposed as a tool to evaluate quantitatively the manner in which water chemistry affects the speciation and biological availability of metals in aquatic systems. (researchgate.net)
FMPs were naturally occurring bacterial ligands that can cause biological effects at nanomolar concentrations. (cdc.gov)

In this work we synthesized 18 biphenylic carboxamides as new CB2-selective ligands and evaluated their pharmacological profiles. (nih.gov)

The boride and borylene motifs tend to have the shortest bonds, typically from 2.00 to 2.15 Å. (wikipedia.org)
What I have found though is that if a ligand has extra bonds in it, it is in all the pdb files generated even though it is not found in the initial input file. (rosettacommons.org)
Although magnesium typically only accepts four ligands, they found THF can add as a fifth, changing the metal's electronic symmetry and helping bonds break and form. (acs.org)
This subject is usually taught after students are introduced to organic chemistry, which concerns the synthesis and reactions of compounds of carbon (typically containing C-H bonds). (wikibooks.org)
X-type ligands donate one electron, requiring oxidation of the metal center to form classical covalent M-X bonds (e.g. (frontiersin.org)

Chemists look at ligand-binding sites as part of drug design. (nature.com)

The signaling cascade following ligand binding is also important in deciding cell fate and potentially initiating necroptosis. (news-medical.net)

However, due to the dative bond character, the metal-boron bond distance can vary greatly depending on the bonding motif, as well as the various ligands attached to the metal. (wikipedia.org)
This assay has high sensitivity and excellent specificity for detection of Chemokine (C-X-C motif) ligand 7 ( CXCL7). (uscnk.com)
No significant cross-reactivity or interference between Chemokine (C-X-C motif) ligand 7 ( CXCL7) and analogues was observed. (uscnk.com)
Matrices listed below were spiked with certain level of recombinant Chemokine (C-X-C motif) ligand 7 ( CXCL7) and the recovery rates were calculated by comparing the measured value to the expected amount of Chemokine (C-X-C motif) ligand 7 ( CXCL7) in samples. (uscnk.com)
Intra-assay Precision (Precision within an assay): 3 samples with low, middle and high level Chemokine (C-X-C motif) ligand 7 ( CXCL7) were tested 20 times on one plate, respectively. (uscnk.com)
Inter-assay Precision (Precision between assays): 3 samples with low, middle and high level Chemokine (C-X-C motif) ligand 7 ( CXCL7) were tested on 3 different plates, 8 replicates in each plate. (uscnk.com)
The linearity of the kit was assayed by testing samples spiked with appropriate concentration of Chemokine (C-X-C motif) ligand 7 ( CXCL7) and their serial dilutions. (uscnk.com)
The microtiter plate provided in this kit has been pre-coated with an antibody specific to Chemokine (C-X-C motif) ligand 7 ( CXCL7). (uscnk.com)
Standards or samples are then added to the appropriate microtiter plate wells with a biotin-conjugated antibody specific to Chemokine (C-X-C motif) ligand 7 ( CXCL7). (uscnk.com)
After TMB substrate solution is added, only those wells that contain Chemokine (C-X-C motif) ligand 7 ( CXCL7), biotin-conjugated antibody and enzyme-conjugated Avidin will exhibit a change in color. (uscnk.com)

While Macrophen and Double Macrophen were the most active substances among polyamino-phenolic ligands, dendrimers were overall twofold more effective than all other compounds with a reduction up to 85 and 73% of legionella and multi-species biofilms, respectively. (frontiersin.org)

But since the metal uses two of its electrons in forming the metal-ligand bond, the Z-ligand raises the valence of the metal center by two units. (wikipedia.org)
However, transition metals also exhibit Lewis-basic character from metal-to-ligand back-donation from partial filling of their upper valence d shell. (frontiersin.org)

Metal-organic networks are typically based upon the cross-linking of transition metal-based nodes by "spacer" organic ligands. (usf.edu)
Investigation of metal-organic networks based upon rigid ligands possessing two types of coordination sites (nicotinate and dinicotinate) and conformationally labile ligands possessing saturated fragments (glutarate and adipate) will be addressed in the context of topological approaches to the design of multi-dimensional networks with particular emphasis upon their resulting properties. (usf.edu)

Since my previous post I decided to try taking the original pdb file (1A52) from the database and dock the native ligand (oestradiol) into it to confirm that the docking is occurring correctly. (rosettacommons.org)
Another question about ligand dock. (rosettacommons.org)
Also, when I do ligand dock, I just copy the ligand to a new pdb file, use babel to convert it to a sdf file, then use the python script to generate params file. (rosettacommons.org)

Typically you throw out the worst 95% of structures by total score without bothering to look at them. (rosettacommons.org)
Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. (rcsb.org)
The main challenges left to be solved is the evaluation of restraint goodness, assigning secondary structures, restraint interconditioning, and water and ligand placement. (helsinki.fi)

Therefore, these Z-ligands can attack at (a) the metal (even in 18 electron compounds), (b) the metal-ligand bond, or (c) the ligands. (wikipedia.org)

The ability of Lewis acids to coordinate to transition metals as σ-acceptor ligands was recognized as early as in the 1970s, but the so-called Z-type ligands remained curiosities until the early 2000s. (wikipedia.org)

KDN21 is a bivalent ligand that contains δ and κ opioid antagonist pharmacophores linked through a 21-atom spacer. (aspetjournals.org)

For one thing, the researchers employed special ligands - chemical chains that extend from the nanocrystals' surfaces and helps facilitate conductivity as they are packed together into a film. (zmescience.com)
Residues from αB-helix and the EF and BG-loops are involved in binding of side chains C-terminal to phosphotyrosine in the ligand. (lu.se)

The concentration of the chemicals tested as anti-biofilm agents was chosen based on cytotoxicity assays: the highest non-cytotoxic chemical concentration was used for biofilm inhibition assays, with dendrimer concentration 10-fold higher than polyamino-phenolic ligands. (frontiersin.org)
Furthermore, the oxazoline (15)N NMR chemical shifts are affected by the trans ligand, with the resonances for the group trans to hydride typically downfield of those trans to η(3)-allyl and tosylamide. (unboundmedicine.com)
These respond to a variety of stimuli, such as voltage, chemical ligands, and mechanical/osmotic stimuli. (lu.se)

I wholeheartedly endorse Blaze to all researchers and pharma companies looking to maximize their ligand-based virtual screening capabilities and drive remarkable advancements in drug discovery. (cresset-group.com)

In this study, the anti-biofilm activity of previously fabricated polyamino-phenolic ligands and polyamidoamine dendrimers was investigated against legionella mono-species and multi-species biofilms formed by L. pneumophila in association with other bacteria that can be found in tap water ( Aeromonas hydrophila , Pseudomonas aeruginosa , Escherichia coli , Klebsiella pneumoniae ). (frontiersin.org)
Additional information concerning risk factors and other matters concerning Ligand can be found in our Ligand's earnings press release, slides and periodic filings with the SEC. Ligand undertakes no obligation to revise or update any statements to reflect events or circumstances after the date of this conference call. (seekingalpha.com)
Chen and his team found a way to strip those ligands away chemically, allowing the clusters to fuse together with just a bit of pressure. (scitechdaily.com)

The experiments consist of kinetic (time- kinetic data is typically not sufficient to constrain the course) measurements after TGF-b stimulation under differ- parameter values to a single optimal solution, and multiple ent conditions: untreated cells and three cases in which parameter sets can explain the available data. (lu.se)

3. names of the topology and parameter files for the ligands. (lu.se)

Typically, these Z-type ligands are Lewis acids, or electron acceptors. (wikipedia.org)
Although many Z-ligands are Lewis acids, they behave as neutral ligands in the complex without contributing to the overall charge present on the complex. (wikipedia.org)
L-type ligands are Lewis bases that donate two electrons to form a dative L → M bond (e.g. (frontiersin.org)

Prior to docking simulations using AutoDock, the drug likeness properties of the ligands were screened using in silico techniques. (ijpsonline.com)
The software utilizes parallelism and is computationally practical with compute requirements on an order of magnitude lower than those typically seen in molecular dynamics simulations. (helsinki.fi)

Use Blaze to find alternatives to typically problematic drug types. (cresset-group.com)
As our most feature-packed software package, both ligand-based and structure-based drug designers are supported to progress their lead optimization, with confidence. (cresset-group.com)

This means that presence of the Z-ligands change the dn configuration of the complex without changing the total e− count. (wikipedia.org)
A Z-ligand is usually accompanied by an L-ligand, as the presence of the L-ligand adds stability to the complex. (wikipedia.org)
In addition to the geometry changes involved in the dative bonding from the metal to the Z-ligand complex, the bond itself can differ greatly depending on the type of buttresses involved. (wikipedia.org)
On the right is a typical reaction of a Z-ligand where the electron deficit BPh3 adds to the anionic Fe complex. (wikipedia.org)
A common configuration is the highly symmetrical octahedral complex, in which six equivalent ligands are bound to the central ion. (wolfram.com)

This is in contrast to X-type ligands, which form a bond with the ligand and metal center each donating one electron, and L-type ligands, which form a bond with the ligand donating two electrons. (wikipedia.org)
A Z‑function ligand interacts with a metal center via a dative covalent bond, differing from the L‑function in that both electrons are donated by the metal rather than the ligand. (wikipedia.org)
As such, Z-ligands donate zero electrons to a metal center because they tend to be strong electron acceptors. (wikipedia.org)
This geometry change can be stabilized by the addition of an L-ligand on the metal center. (wikipedia.org)
Typically, the donor buttresses with sulfur and nitrogen donor ligands have metal-boron bond lengths of 2.05-2.25 Å, and donor buttresses with phosphorus donor ligands have metal-boron bond lengths of 2.17-2.91 Å. (wikipedia.org)

This article intends to give an educational overview on the current status of PSMA ligand PET imaging, including imaging procedure and interpretation, clinical indications, diagnostic potential, and impact on treatment planning. (snmjournals.org)
In addition, the advent of immunotherapies, specifically, agents that target cytotoxic T-lymphocyte antigen-4, anti-programmed death-1, and programmed death ligand-1, has increased the potential therapeutic options available to patients with both systemic and brain disease. (medscape.com)

In cases of single metastatic lesions or large, symptomatic lesions in oligometastatic disease, resection is typically advised. (medscape.com)

Atezolizumab 840mg IV q2Weeks, 1200 mg IV q3Weeks, or 1680 mg IV q4Weeks for up to 1 year (for completely resected IIB-IIIA or high-risk stage IIA programmed death ligand 1 (PD-L1) ≥1% NSCLC in patients who previously received adjuvant chemotherapy. (medscape.com)

Typically, after 2-8 y of ADT, prostate-specific antigen (PSA) begins to rise again, indicating metastatic castration-resistant PC, the lethal form of the disease. (snmjournals.org)

The other issue to consider is that RosettaLigand is typically run with a small amount (10-15 degrees or so) of torsional freedom in the ligand. (rosettacommons.org)

Sensitivity The minimum detectable dose of this kit is typically less than 1.47pg/mL. (uscnk.com)
The modified HPLC method did not have sufficient sensitivity to detect fMLP in environmental air samples, which typically contained only a few milligrams of total dust. (cdc.gov)

Minor infections, typically of the upper respiratory tract, are common triggers for SCLS, although an infection-related prodrome is identified in only 44%-65% of cases ( 2 , 3 ). (cdc.gov)

Monoclonal antibodies have proven typically too fragile to withstand the elution and cleaning procedures, prove sensitive to protease attack and exhibit difficulties with discrete antibody affinities preventing target elution without damaging the product from some systems, such as in cell purification screens. (avacta.com)

Anatomy26

Organisms12

Diseases2

Chemicals and Drugs125

Analytical, Diagnostic and Therapeutic Techniques and Equipment34

Phenomena and Processes57

Disciplines and Occupations3

Information Science7

Molecules12

Protein14

Receptor10

Ambiphilic ligands3

Tumor2

Interactions7

Binds1

Conformational changes1

Atoms5

Pair of electrons2

Affinity5

Electrons from the metal1

Receptors2

Complexes4

Interaction1

Stabilize3

Proteins2

Bind1

Electron-deficient1

Biological2

Pharmacological1

Bonds5

Chemists1

Signaling cascade1

Motif10

Substances1

Valence2

Organic2

Dock3

Structures3

Compounds1

Transition metals1

Atom1

Chains2

Chemical3

Researchers1

Found3

Measurements1

Parameter1

Lewis3

Simulations2

Drug2

Complex5

Metal5

Potential2

Large1

Death1

Form1

Small1

Sensitivity2

Common1

Target1