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Protocols

PDB-Ligand specifications

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Unique identifier OMICS_04576
Name PDB-Ligand
Restrictions to use None
Maintained No

Publication for PDB-Ligand

PDB-Ligand citations

 (22)
library_books

How Diverse Are the Protein Bound Conformations of Small Molecule Drugs and Cofactors?

2018
PMCID: 5880911
PMID: 29637066
DOI: 10.3389/fchem.2018.00068

[…] of 4,548 unique small molecules. Ninety-one ligands in this dataset are represented by at least 10 structures, and these served as the basis of this analysis.To ensure that all ligands with the same PDB ligand ID have identical stereochemistry, their isomeric smiles (generated with UNICON, Sommer et al., ) were compared in order to keep only the isomer with the most occurrences. The Approved Drug […]

call_split

Structural Basis for the Substrate Inhibition of Proline Utilization A by Proline

2017
PMCID: 5786444
PMID: 29295473
DOI: 10.3390/molecules23010032
call_split See protocol

[…] ion was carried out using MOLPROBITY []. The final model includes 1949 out of the expected 2002 amino acid residues in the asymmetric unit. Each BjPutA protomer contains a reduced FAD (occupancy = 1; PDB ligand code FDA). Two residues were modeled with dual side chain conformations (Arg146 and Ser214). The solvent model includes 719 water molecules (occupancy = 1) and 14 sulfate ions (occupancy = […]

library_books

Structure based drug discovery for designing leads for the non toxic metabolic targets in multi drug resistant Mycobacterium tuberculosis

2017
J Transl Med
PMCID: 5740895
PMID: 29268770
DOI: 10.1186/s12967-017-1363-9

[…] MetaCyc. Of these 33 targets, 15 with available crystal structures were utilized for the Molecular Docking studies. The GLIDE suite of Schrodinger for the corresponding natural substrate (NS, if any)/PDB ligand was used to determine the binding poses for each protein structure of the shortlisted 15 targets.Based on the understanding of the active site of the proteins, libraries of compounds (avera […]

library_books

Searching for bioactive conformations of drug like ligands with current force fields: how good are we?

2017
J Cheminform
PMCID: 5432473
DOI: 10.1186/s13321-017-0216-0

[…] the OPLS3 force field.Quite surprisingly, a rather narrow parameter set of the AMBER* force field focusing primarily on proteins and nucleic acids instead of on small molecules performed well on our PDB ligand selection (especially with less flexible ligands), closely followed by the MMFF94s and OPLS_2005 force fields (ranking by the total sum of the best RMSDs; Additional file : Table S6).As can […]

library_books

Cloning retinoid and peroxisome proliferator activated nuclear receptors of the Pacific oyster and in silico binding to environmental chemicals

2017
PLoS One
PMCID: 5398557
PMID: 28426724
DOI: 10.1371/journal.pone.0176024

[…] s of human RXR, RAR or PPAR LBD in complex with either 9RA (1FBY [], 3LBD []), ATRA (2LBD []), TTNPB (1XAP []), TBT (3E94 []) or rosiglitazone (4EMA []) were obtained from the RCSB Protein Data Bank (PDB) []. Ligand dictionaries for docking were also obtained from the PDB site including the molecular structure of estradiol for negative control. C. gigas, R. clavigera and N. lapillus models for RXR […]

library_books

The polypharmacology browser: a web based multi fingerprint target prediction tool using ChEMBL bioactivity data

2017
J Cheminform
PMCID: 5319934
PMID: 28270862
DOI: 10.1186/s13321-017-0199-x

[…] rawn or copy-pasted in SMILES or sdf file format. An option is available to extract the query molecule from the Protein Data Bank (PDB) using the PDB id of the protein–ligand complex of interest (the PDB ligand data was downloaded from http://ligand-expo.rcsb.org/ website in March 2016 and stored on our web server, and will be updated once a year). The option “No. of targets” allows the user to in […]


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PDB-Ligand institution(s)
Research and Development, IDR Tech B-3003 Tripolis, BunDang-Ku, SungNam-Shi, KyungKi-Do, Korea

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