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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:

3jsx

2.450 Å

X-ray

2009-09-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:NAD(P)H dehydrogenase [quinone] 1
ID:NQO1_HUMAN
AC:P15559
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:1.6.5.2


Chains:

Chain Name:Percentage of Residues
within binding site
D8 %
E48 %
G44 %


Ligand binding site composition:

B-Factor:67.230
Number of residues:25
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.2891336.500

% Hydrophobic% Polar
55.3044.70
According to VolSite

Ligand :
3jsx_5 Structure
HET Code: CC2
Formula: C22H17O3
Molecular weight: 329.369 g/mol
DrugBank ID: -
Buried Surface Area:65.73 %
Polar Surface area: 49.36 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 0
Rings: 4
Aromatic rings: 3
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
35.1488-55.63421.5195


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
C11CE3TRP- 1053.330Hydrophobic
C12CE2TRP- 1053.810Hydrophobic
C11CE2PHE- 1063.720Hydrophobic
C12CZTYR- 1263.810Hydrophobic
C13CE1TYR- 1284.180Hydrophobic
C17CBTYR- 1284.240Hydrophobic
DuArDuArTYR- 1283.880Aromatic Face/Face
C18CEMET- 1313.550Hydrophobic
C19CEMET- 1543.810Hydrophobic
O2NE2HIS- 1613.14134.5H-Bond
(Protein Donor)
O7NE2HIS- 1613.18161.42H-Bond
(Protein Donor)
C11CE2PHE- 1783.640Hydrophobic
C12C6FAD- 6013.50Hydrophobic