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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:

3ox1

2.000 Å

X-ray

2010-09-21

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
A52 %
B48 %


Ligand binding site composition:

B-Factor:21.381
Number of residues:29
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.056553.500

% Hydrophobic% Polar
56.1043.90
According to VolSite

Ligand :
3ox1_1 Structure
HET Code: 695
Formula: C15H18N2O3S
Molecular weight: 306.380 g/mol
DrugBank ID: -
Buried Surface Area:66.85 %
Polar Surface area: 83.65 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-4.24581-5.12176-15.0057


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
C20CG2VAL- 694.140Hydrophobic
C16CE2PHE- 1264.40Hydrophobic
C2CZPHE- 1263.180Hydrophobic
C13CD1ILE- 1283.490Hydrophobic
C13CE1PHE- 1313.820Hydrophobic
C13CZPHE- 1784.190Hydrophobic
C10CZPHE- 1783.450Hydrophobic
C1C1'FAD- 2323.90Hydrophobic
O3OHOH- 2642.62179.94H-Bond
(Protein Donor)