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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:

1rkp

2.050 Å

X-ray

2003-11-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:cGMP-specific 3',5'-cyclic phosphodiesterase
ID:PDE5A_HUMAN
AC:O76074
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:27.686
Number of residues:20
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.762641.250

% Hydrophobic% Polar
51.0548.95
According to VolSite

Ligand :
1rkp_1 Structure
HET Code: IBM
Formula: C10H14N4O2
Molecular weight: 222.244 g/mol
DrugBank ID: DB07954
Buried Surface Area:62.37 %
Polar Surface area: 69.3 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 1
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
43.765915.553848.4273


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
C13CD2TYR- 6123.920Hydrophobic
C11CD1LEU- 7254.490Hydrophobic
C10CBALA- 7673.880Hydrophobic
C10CBILE- 7684.450Hydrophobic
C13CG1VAL- 7824.430Hydrophobic
C12CZPHE- 7863.610Hydrophobic
N7OE1GLN- 8172.68174.78H-Bond
(Ligand Donor)
O6NE2GLN- 8172.89165.36H-Bond
(Protein Donor)
C10CE2PHE- 8203.980Hydrophobic
C11CE1PHE- 8203.960Hydrophobic
DuArDuArPHE- 8203.760Aromatic Face/Face