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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:

3kft

2.100 Å

X-ray

2009-10-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pentaerythritol tetranitrate reductase
ID:P71278_ENTCL
AC:P71278
Organism:Enterobacter cloacae
Reign:Bacteria
TaxID:550
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A72 %
B28 %


Ligand binding site composition:

B-Factor:29.931
Number of residues:35
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 3
Water Molecules: 3
Cofactors: FMN FMN NAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0931397.250

% Hydrophobic% Polar
39.6160.39
According to VolSite

Ligand :
3kft_2 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:48.96 %
Polar Surface area: 343.54 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
-10.034913.9188-47.2049


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
N7NOG1THR- 262.91134.31H-Bond
(Ligand Donor)
C4NCBTHR- 264.220Hydrophobic
O7NNE2HIS- 1812.75167.66H-Bond
(Protein Donor)
O7NND1HIS- 1842.95166.32H-Bond
(Protein Donor)
C5DCGGLN- 2414.460Hydrophobic
O3DNH2ARG- 3243.4156.26H-Bond
(Protein Donor)
C2BCBPRO- 3473.720Hydrophobic
C2BCE2PHE- 3503.960Hydrophobic
C2DC9FMN- 3653.580Hydrophobic
C1BC1BNAD- 3663.650Hydrophobic
N1AOHOH- 5053.25123.2H-Bond
(Protein Donor)