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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:

2wzw

1.800 Å

X-ray

2009-12-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Nitroreductase NfnB
ID:NFNB_MYCS2
AC:A0R6D0
Organism:Mycobacterium smegmatis 155)
Reign:Bacteria
TaxID:246196
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A94 %
B6 %


Ligand binding site composition:

B-Factor:29.819
Number of residues:36
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors: FMN
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.129452.250

% Hydrophobic% Polar
29.1070.90
According to VolSite

Ligand :
2wzw_2 Structure
HET Code: NDP
Formula: C21H26N7O17P3
Molecular weight: 741.389 g/mol
DrugBank ID: DB02338
Buried Surface Area:48.79 %
Polar Surface area: 404.9 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 5
Rings: 5
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
-15.2629-71.3847-19.2222


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
C5DCE1TYR- 924.290Hydrophobic
C5NCBTYR- 9240Hydrophobic
O2NNEARG- 1053.19134.75H-Bond
(Protein Donor)
O2NNH2ARG- 1052.69160.17H-Bond
(Protein Donor)
O2NCZARG- 1053.360Ionic
(Protein Cationic)
C3BCGARG- 1053.990Hydrophobic
C5BCE2PHE- 1084.380Hydrophobic
O1AOHTYR- 1132.86161.7H-Bond
(Protein Donor)
N6AOILE- 1183.17142.38H-Bond
(Ligand Donor)
C2DCD1LEU- 1824.450Hydrophobic
C4DCBLEU- 1824.360Hydrophobic
DuArDuArPHE- 1853.790Aromatic Face/Face
N3AOHOH- 20932.81149.52H-Bond
(Protein Donor)