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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:

1mc0

2.860 Å

X-ray

2002-08-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:cGMP-dependent 3',5'-cyclic phosphodiesterase
ID:PDE2A_MOUSE
AC:Q922S4
Organism:Mus musculus
Reign:Eukaryota
TaxID:10090
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:90.383
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.612273.375

% Hydrophobic% Polar
61.7338.27
According to VolSite

Ligand :
1mc0_1 Structure
HET Code: PCG
Formula: C10H11N5O7P
Molecular weight: 344.197 g/mol
DrugBank ID: -
Buried Surface Area:81.72 %
Polar Surface area: 183.16 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 3
Rings: 4
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 1

Mass center Coordinates

XYZ
127.77357.2502118.275


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
O2'OHOH- 22.91179.99H-Bond
(Protein Donor)
N7OGSER- 4242.68159.03H-Bond
(Protein Donor)
O6NASP- 4392.75154.65H-Bond
(Protein Donor)
N1OD1ASP- 4392.6166.44H-Bond
(Ligand Donor)
N2OD1ASP- 4393.4127.64H-Bond
(Ligand Donor)
C5'CD1ILE- 4524.10Hydrophobic
O2ANILE- 4582.52156.42H-Bond
(Protein Donor)
C2'CE1PHE- 4804.480Hydrophobic
O1ANTYR- 4812.96130.17H-Bond
(Protein Donor)
C5'CD2TYR- 4814.410Hydrophobic
C1'CG1VAL- 4843.850Hydrophobic
C5'CG2VAL- 4843.420Hydrophobic
C2'CG2THR- 4924.40Hydrophobic
O2'OG1THR- 4922.75164.52H-Bond
(Ligand Donor)
C2'CD1ILE- 4954.040Hydrophobic