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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:

4g2l

3.000 Å

X-ray

2012-07-12

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
ID:PDE9A_HUMAN
AC:O76083
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:33.574
Number of residues:27
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: ZN MG

Cavity properties

LigandabilityVolume (Å3)
1.128880.875

% Hydrophobic% Polar
55.5644.44
According to VolSite

Ligand :
4g2l_2 Structure
HET Code: 0WL
Formula: C19H24N7O
Molecular weight: 366.440 g/mol
DrugBank ID: -
Buried Surface Area:44.79 %
Polar Surface area: 89.5 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 5
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
97.545521.877611.8205


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
C10CGMET- 3653.740Hydrophobic
C12CG2ILE- 4034.460Hydrophobic
C18CD2LEU- 4203.850Hydrophobic
C13CD2LEU- 4203.870Hydrophobic
C18CD2LEU- 4214.320Hydrophobic
C16CE2TYR- 4244.210Hydrophobic
C18CE2TYR- 4243.850Hydrophobic
N26OHTYR- 4243.28159.71H-Bond
(Ligand Donor)
C1CBPHE- 4414.420Hydrophobic
C16CD1PHE- 4413.780Hydrophobic
C18CBALA- 4523.890Hydrophobic
N25OE1GLN- 4532.72163.31H-Bond
(Ligand Donor)
O27NE2GLN- 4533.04175.62H-Bond
(Protein Donor)