Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 4

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Identification of hot-spot residues in protein-protein interactions by computational docking.

(2008) BMC Bioinformatics 9

PubMed: 18939967 | PubMedCentral: PMC2579439 | DOI: 10.1186/1471-2105-9-447

Table 1 Initial dataset of complexes used in this work Complex a Res b Receptor Ligand Unbound receptor Res b Unbound ligand Res b Complex type c 1A22 2.60 Growth hormone receptor Growth hormone - - 1... GU 2.50 B/U 1A4Y 2.00 Ribonuclease inhibitor Angiogenin - - 1UN3 1.70 B/U 1AHW 3.00 Fab 5G9 Tissue Factor 1K6Q 2.40 2HFT 1.69 U/U 1AIE 1.50 p53 p53 - - - - B/B 1BRS 2.00 Barnase Barstar 1A2P 1.50 - - U/B 1BXI 2.05 Colicin E9 Immunity protein Im9 1FSJ 1.80 - - U/B 1DAN 2.00 Tissue Factor Factor VII 2HFT 1.69 - - U/B 1DFJ 2.30 Ribonuclease A Ribonuclease inhibitor 1FS3 1.40 2BNH 2.30 U/U 1DN2 2.70 IgG1 Fc fragment DCAWHLGELV WCT-NH 2 1H3V 3.10 - - U/B 3HFM 3.00 HYHEL-10 HEL 1GPO 1.95 3LZT 0.92 U/U 1GC1 2.50 CD4 gp120 1CDJ 2.50 - - U/B 1F47 1.95 Zipa FTSZ fragment 1F7W NMR - - U/B 1FC2 2.80 Fc fragment Protein A - - - - B/B 1FCC 3.50 Fc fragment Protein G 1H3V 3.10 - - U/B 1IAR 2.60 IL-4 receptor IL-4 - - 1HIK 2.60 B/U 1JCK 3.50 T-cell antigen receptor SEC3 1BEC 1.70 1CK1 2.60 U/U 1JRH 2.80 Antibody A6 Interferon-γ receptor - - - - B/B 1JTD 2.30 TEM-1 β-lactamase BLIP 1ZG4 1.55 - - U/B 1NMB 2.50 NC10 Neuraminidase N9 - - 7NN9 2.00 B/U 2PTC 1.90 Trypsin BPTI 1S0Q 1.02 1G6X 0.86 U/U 1VFB 1.80 Antibody D1.3 HEL - - 3LZT 0.92 B/U a PDB Code, b Resolution in Å; c B, Bound; U, Unbound For most of the complexes, the structure of only one of the two partners is available in the unbound conformation.

Publication Year: 2008


Rapid and accurate prediction and scoring of water molecules in protein binding sites.

(2012) PLoS One 7

PubMed: 22396746 | PubMedCentral: PMC3291545 | DOI: 10.1371/journal.pone.0032036

Protein PDB codes Resolution (Å) Ligand HIV-Protease 3FX5, 1HPX, 2ZYE a 0.93, 2,1.9 KNI-272 Ribonuclease A 1KF5, 1FS3, 5RSA a 1.2, 1.4, 2 None GluR2 ligand binding core 1FTM b , 1MY2 b 1.7, 1.... AMPA Trypsin 1S0Q, 1UTQ, 1TPO 1.0, 1.2, 1.7 None Concanavalin A 1NLS, 1GKB, 1JBC, 1QNY a 0.9, 1.6, 1.2, 1.8 None Glutathione S-transferase 1K3Y b , 1K3L b 1.3, 1,5 S-hexyl glutatione Carbonic Anhydrase 3KS3, 3MWO, 2ILI 0.9, 1.4, 1.1 None a Structures that have been determined by neutron diffraction.

Publication Year: 2012


Sanjeevini: a freely accessible web-server for target directed lead molecule discovery.

(2012) BMC Bioinformatics 13 Suppl 17

PubMed: 23282245 | PubMedCentral: PMC3521208 | DOI: 10.1186/1471-2105-13-S17-S7

PDBID a Ligand (Molecular formula) EXBFE (kcal/mol)# PBFE (kcal/mol) b PBFE (kcal/mol) c 1 1BRA C 7 H 8 N 2 -2.496 -4.92 -4.59 2 1F0T C 19 H 19 N 5 O 4 S 2 -8.29 -6.92 -7.35 3 1F0U C 27 H 30 N 4 O 3 -... .89 -8.98 -6.96 4 1MTW C 26 H 28 N 4 O 3 -10.076 -7.84 -6.64 5 1PPC C 27 H 31 N 5 O 4 S -8.8 -8.46 -6.85 6 1TNH C 7 H 9 FN -4.59 -4.49 -4.28 7 1TNI C 10 H 15 N -2.32 -3.74 -3.53 8 1TNJ C 8 H 12 N -2.67 -3.72 -3.77 9 1TNK C 9 H 14 N -2.03 -3.81 -3.51 10 1TNL C 9 H 12 N -2.56 -3.56 -3.99 11 1TPP C 10 H 12 N 2 O 3 -7.95 -6.05 -5.55 12 3PTB C 7 H 8 N 2 -6.46 -5.36 -5.27 13 1S0R / 1S0Q C 8 H 10 N 3 O 1 -5.71 -5.25 -5.59 14 1S0R / 1S0Q C8H11N2O1 -6.04 -5.37 -5.51 15 1S0R / 1S0Q C7H10N3 -6.95 -5.16 -5.99 16 1S0R / 1S0Q C7H9N2 -6.35 -5.26 -5.12 17 1S0R / 1S0Q C8H11N2 -6.59 -5.33 -5.56 18 1S0R / 1S0Q C9H13N2 -6.07 -5.01 -5.41 19 1S0R / 1S0Q C10H15N2 -6.14 -5 -5.55 20 1S0R / 1S0Q C 10 H 15 N 2 (iso) -5.42 -5.26 -5.79 21 1S0R / 1S0Q C 11 H 17 N 2 -6.26 -5 -6.08 22 1S0R / 1S0Q C 12 H 19 N 2 -6.5 -5.45 -6.55 23 1S0R / 1S0Q C 13 H 21 N 2 -6.97 -5.82 -6.53 # Experimental binding free energies of trypsin binding molecules.

For Bovine pancreatic trypsin receptor, a structure with unknown binding site information (PDBID 1S0Q ) is also available in the literature [ 128 , 129 ] along with a protein-ligand complex (PDBID 1S0R ) which was taken as an input in the first case study.

We visualized the docked structures obtained from the above blind docking studies of trypsin inhibitors against the target (PDB ID 1S0Q ) to make sure if the top ranked docked structures have the native ligand pose restored in the native binding site of target.

Publication Year: 2012


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4430139

These residues also form the catalytic triad in the active sites of serine proteases, bovine pancreas trypsin (PDB: 1S0Q), subtilisin (PDB: 2SIC), and carboxypeptidase Y (CPY; PDB: 1YSC).

Publication Year: 2015