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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:

4fcd

2.020 Å

X-ray

2012-05-24

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
A100 %


Ligand binding site composition:

B-Factor:36.698
Number of residues:33
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors:
Metals: ZN MG

Cavity properties

LigandabilityVolume (Å3)
0.961732.375

% Hydrophobic% Polar
51.1548.85
According to VolSite

Ligand :
4fcd_1 Structure
HET Code: 0T6
Formula: C18H15ClN4O2
Molecular weight: 354.790 g/mol
DrugBank ID: -
Buried Surface Area:55.21 %
Polar Surface area: 61.54 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 0
Rings: 4
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
20.6452-11.0909-35.3962


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
C1CZTYR- 5144.450Hydrophobic
C8CD2LEU- 6254.190Hydrophobic
C9CBLEU- 6254.160Hydrophobic
C8CD2LEU- 6653.740Hydrophobic
C1CG1VAL- 6684.040Hydrophobic
C1CD1ILE- 6823.540Hydrophobic
CL1CG2ILE- 6824.120Hydrophobic
CL1CZPHE- 6863.460Hydrophobic
C17SDMET- 7034.250Hydrophobic
C18SDMET- 7033.690Hydrophobic
C15SDMET- 7033.650Hydrophobic
N2NE2GLN- 7163.1174.47H-Bond
(Protein Donor)
C16CBPHE- 7194.380Hydrophobic
C17CBPHE- 7193.70Hydrophobic
DuArDuArPHE- 7193.940Aromatic Face/Face