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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:

3nhj

2.330 Å

X-ray

2010-06-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Ribosyldihydronicotinamide dehydrogenase [quinone]
ID:NQO2_HUMAN
AC:P16083
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A56 %
B44 %


Ligand binding site composition:

B-Factor:40.709
Number of residues:25
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.964502.875

% Hydrophobic% Polar
56.3843.62
According to VolSite

Ligand :
3nhj_1 Structure
HET Code: A2Z
Formula: C12H11NO3
Molecular weight: 217.221 g/mol
DrugBank ID: -
Buried Surface Area:65.27 %
Polar Surface area: 38.77 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 0
Rings: 3
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
-3.71625-6.917-15.8821


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
C15CE3TRP- 10540Hydrophobic
C15CE1PHE- 1063.890Hydrophobic
C12CZPHE- 1264.250Hydrophobic
O3ND2ASN- 1612.82154.24H-Bond
(Protein Donor)
C15CD1PHE- 1783.550Hydrophobic
C12C1'FAD- 2323.570Hydrophobic
C4C1'FAD- 2323.990Hydrophobic