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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:

4ajg

2.300 Å

X-ray

2012-02-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
ID:PDE10_HUMAN
AC:Q9Y233
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.1.4.17


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:36.703
Number of residues:18
Including
Standard Amino Acids: 17
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.081904.500

% Hydrophobic% Polar
57.4642.54
According to VolSite

Ligand :
4ajg_2 Structure
HET Code: F07
Formula: C10H6N2S
Molecular weight: 186.233 g/mol
DrugBank ID: -
Buried Surface Area:53.45 %
Polar Surface area: 54.02 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 0
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
42.3575-2.7195418.6375


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
C1CG1VAL- 6784.110Hydrophobic
C1CD1ILE- 6923.540Hydrophobic
C5CD1ILE- 6924.380Hydrophobic
S11CZPHE- 6964.180Hydrophobic
N7NE2GLN- 7262.77167.43H-Bond
(Protein Donor)
S11CZPHE- 7293.720Hydrophobic
DuArDuArPHE- 7293.640Aromatic Face/Face
DuArDuArPHE- 7293.640Aromatic Face/Face