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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:

2pnc

2.400 Å

X-ray

2007-04-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Primary amine oxidase, liver isozyme
ID:AOCX_BOVIN
AC:Q29437
Organism:Bos taurus
Reign:Eukaryota
TaxID:9913
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:25.410
Number of residues:26
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors:
Metals: CU

Cavity properties

LigandabilityVolume (Å3)
1.298965.250

% Hydrophobic% Polar
53.5046.50
According to VolSite

Ligand :
2pnc_1 Structure
HET Code: CLU
Formula: C9H10Cl2N3
Molecular weight: 231.102 g/mol
DrugBank ID: DB00575
Buried Surface Area:71.42 %
Polar Surface area: 38.03 Å2
Number of
H-Bond Acceptors: 0
H-Bond Donors: 3
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
35.2397-10.844642.2997


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
CL2CBALA- 3693.470Hydrophobic
CAFCE2TYR- 3833.670Hydrophobic
NAJOD2ASP- 3852.97157.53H-Bond
(Ligand Donor)
NAHOD1ASP- 3852.88136.35H-Bond
(Ligand Donor)
CAFCE1PHE- 3884.440Hydrophobic
CL1CGMET- 4673.540Hydrophobic
CAFSDMET- 46740Hydrophobic
CL1CE1TYR- 4723.730Hydrophobic
CL2CZTYR- 4724.390Hydrophobic
DuArDuArTYR- 4723.60Aromatic Face/Face