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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:

3gam

1.980 Å

X-ray

2009-02-17

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
A32 %
B68 %


Ligand binding site composition:

B-Factor:26.440
Number of residues:23
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.581583.875

% Hydrophobic% Polar
47.4052.60
According to VolSite

Ligand :
3gam_2 Structure
HET Code: MXX
Formula: C13H15NO3
Molecular weight: 233.263 g/mol
DrugBank ID: DB08228
Buried Surface Area:59.62 %
Polar Surface area: 38.77 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 0
Rings: 2
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
23.4367-16.9914-15.1016


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
C14CH2TRP- 1053.360Hydrophobic
C15CZ3TRP- 1054.130Hydrophobic
C15CE1PHE- 1064.350Hydrophobic
C14CZPHE- 1263.630Hydrophobic
O17ND2ASN- 1612.86166.37H-Bond
(Protein Donor)
C14CE2PHE- 1784.350Hydrophobic
C15CE1PHE- 1783.470Hydrophobic
C13C1'FAD- 2324.130Hydrophobic
C14C6FAD- 2323.620Hydrophobic
C5C1'FAD- 2323.670Hydrophobic