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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:

2o8h

1.800 Å

X-ray

2006-12-12

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
ID:PDE10_RAT
AC:Q9QYJ6
Organism:Rattus norvegicus
Reign:Eukaryota
TaxID:10116
EC Number:3.1.4.17


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:32.359
Number of residues:25
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.959705.375

% Hydrophobic% Polar
55.5044.50
According to VolSite

Ligand :
2o8h_1 Structure
HET Code: 227
Formula: C24H30N5O4S
Molecular weight: 484.591 g/mol
DrugBank ID: -
Buried Surface Area:39.43 %
Polar Surface area: 97.68 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
11.674221.132641.7134


Binding mode :
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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
C20CD2LEU- 6253.930Hydrophobic
C28CZPHE- 6293.160Hydrophobic
C21CG1VAL- 6683.660Hydrophobic
C7CG2ILE- 6824.470Hydrophobic
C21CD1ILE- 6824.230Hydrophobic
C18CZTYR- 6834.330Hydrophobic
C4SDMET- 7033.940Hydrophobic
C18SDMET- 7033.780Hydrophobic
C29SDMET- 7033.960Hydrophobic
C10SDMET- 7033.610Hydrophobic
C11CEMET- 7033.790Hydrophobic
O17NE2GLN- 7163.09158.13H-Bond
(Protein Donor)
C21CD2PHE- 7193.750Hydrophobic
C18CBPHE- 7193.840Hydrophobic
C10CD1PHE- 7194.280Hydrophobic
C1CE1PHE- 7193.480Hydrophobic
C9CBPHE- 7193.760Hydrophobic
DuArDuArPHE- 7193.540Aromatic Face/Face
C23CG2VAL- 7233.950Hydrophobic