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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:

4zvm

1.970 Å

X-ray

2015-05-18

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
A53 %
B47 %


Ligand binding site composition:

B-Factor:23.084
Number of residues:32
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.954573.750

% Hydrophobic% Polar
52.9447.06
According to VolSite

Ligand :
4zvm_1 Structure
HET Code: DM2
Formula: C27H28NO11
Molecular weight: 542.511 g/mol
DrugBank ID: DB00997
Buried Surface Area:50.2 %
Polar Surface area: 213.34 Å2
Number of
H-Bond Acceptors: 11
H-Bond Donors: 4
Rings: 5
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 5

Mass center Coordinates

XYZ
48.84315.4510513.9388


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
C21CH2TRP- 1053.460Hydrophobic
N3'OE1GLN- 1222.93160.45H-Bond
(Ligand Donor)
C21CE1PHE- 1263.680Hydrophobic
C15CEMET- 1544.130Hydrophobic
C17SDMET- 1544.360Hydrophobic
O19ND2ASN- 1613.2171.63H-Bond
(Protein Donor)
DuArDuArPHE- 1783.710Aromatic Face/Face
C14CG2ILE- 1943.890Hydrophobic
C6'CG2ILE- 1944.060Hydrophobic
C11CG2ILE- 1943.670Hydrophobic
C21C6FAD- 3023.550Hydrophobic