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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:

1oo6

2.000 Å

X-ray

2003-03-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Oxygen-insensitive NAD(P)H nitroreductase
ID:NFSB_ECOLI
AC:P38489
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A52 %
B48 %


Ligand binding site composition:

B-Factor:32.701
Number of residues:22
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: FMN
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.626553.500

% Hydrophobic% Polar
50.0050.00
According to VolSite

Ligand :
1oo6_1 Structure
HET Code: SN2
Formula: C11H12Cl2N4O5
Molecular weight: 351.143 g/mol
DrugBank ID: DB03228
Buried Surface Area:54.45 %
Polar Surface area: 137.96 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 1
Rings: 1
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 2
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-9.70414-14.510850.0306


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
O5NZLYS- 143.050Ionic
(Protein Cationic)
O3NTHR- 413.29127.38H-Bond
(Protein Donor)
C8CE1PHE- 704.240Hydrophobic
CL1CD1PHE- 703.760Hydrophobic
CL2CDLYS- 1194.340Hydrophobic
N4OGLY- 1203.43161.67H-Bond
(Ligand Donor)
O3O2'FMN- 2203.04171.8H-Bond
(Protein Donor)