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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4pgt

2.100 Å

X-ray

1999-03-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glutathione S-transferase P
ID:GSTP1_HUMAN
AC:P09211
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.5.1.18


Chains:

Chain Name:Percentage of Residues
within binding site
A9 %
B91 %


Ligand binding site composition:

B-Factor:21.553
Number of residues:33
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.783911.250

% Hydrophobic% Polar
40.7459.26
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4pgtHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
4pgt_2 Structure
HET Code: GBX
Formula: C30H26N3O9S
Molecular weight: 604.607 g/mol
DrugBank ID: -
Buried Surface Area:55.7 %
Polar Surface area: 245.77 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 4
Rings: 5
Aromatic rings: 4
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 11

Mass center Coordinates

XYZ
21.93235.4206329.0517
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4pgtRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation8051015Highcharts.com


Binding mode :
What is Poseview ?
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C10CZTYR- 74.270Hydrophobic
SG2CE1TYR- 73.410Hydrophobic
CB2CE2PHE- 83.550Hydrophobic
C5'CBPHE- 83.960Hydrophobic
C6'CBPHE- 84.30Hydrophobic
C6'CG1VAL- 104.320Hydrophobic
C5'CG2VAL- 103.560Hydrophobic
O12CZARG- 133.950Ionic
(Protein Cationic)
O8NEARG- 132.95165.85H-Bond
(Protein Donor)
C9CGARG- 133.40Hydrophobic
CB1CDARG- 134.070Hydrophobic
SG2CGARG- 134.150Hydrophobic
C7'CG1VAL- 354.360Hydrophobic
O31NE1TRP- 383.19145.75H-Bond
(Protein Donor)
O32NZLYS- 443.550Ionic
(Protein Cationic)
CG1CBGLN- 514.160Hydrophobic
O32NE2GLN- 512.64161.03H-Bond
(Protein Donor)
O2NLEU- 522.63162.26H-Bond
(Protein Donor)
N2OLEU- 522.59150.18H-Bond
(Ligand Donor)
O11OGSER- 653.39146.02H-Bond
(Protein Donor)
O11NSER- 652.91159.78H-Bond
(Protein Donor)
O12OGSER- 652.74136.35H-Bond
(Protein Donor)
O12NSER- 653.38143.64H-Bond
(Protein Donor)
N1OD1ASP- 983.360Ionic
(Ligand Cationic)
N1OD2ASP- 982.610Ionic
(Ligand Cationic)
N1OD2ASP- 982.61146.71H-Bond
(Ligand Donor)
C7CE2TYR- 1084.040Hydrophobic
C11CZTYR- 1083.290Hydrophobic