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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:

2vcx

2.100 Å

X-ray

2007-09-27

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:6.5206.9006.9000.3807.2902

List of CHEMBLId :

CHEMBL261777


Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Hematopoietic prostaglandin D synthase
ID:HPGDS_HUMAN
AC:O60760
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:22.404
Number of residues:22
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9021687.500

% Hydrophobic% Polar
38.6061.40
According to VolSite

Ligand :
2vcx_2 Structure
HET Code: D26
Formula: C12H9N3S
Molecular weight: 227.285 g/mol
DrugBank ID: DB07614
Buried Surface Area:63.17 %
Polar Surface area: 69.81 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
32.7614-6.72219-17.2521


Binding mode :
What is Poseview ?
  • 2D View
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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
S3CGARG- 143.970Hydrophobic
C18CGARG- 143.470Hydrophobic
C15CEMET- 994.240Hydrophobic
C17CBMET- 993.390Hydrophobic
DuArDuArTRP- 1043.830Aromatic Face/Face
DuArDuArTRP- 1043.830Aromatic Face/Face
C15CG2ILE- 1554.460Hydrophobic
C16SGCYS- 15640Hydrophobic