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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:

4kqw

1.390 Å

X-ray

2013-05-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Ketol-acid reductoisomerase (NADP(+))
ID:ILVC_SLAES
AC:D0WGK0
Organism:Slackia exigua
Reign:Bacteria
TaxID:649764
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A87 %
B13 %


Ligand binding site composition:

B-Factor:13.310
Number of residues:59
Including
Standard Amino Acids: 52
Non Standard Amino Acids: 2
Water Molecules: 5
Cofactors:
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
0.816661.500

% Hydrophobic% Polar
46.4353.57
According to VolSite

Ligand :
4kqw_1 Structure
HET Code: NAP
Formula: C21H25N7O17P3
Molecular weight: 740.381 g/mol
DrugBank ID: DB03461
Buried Surface Area:58.27 %
Polar Surface area: 405.54 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 5
Rings: 5
Aromatic rings: 3
Anionic atoms: 4
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
-12.22791.89773-14.9665


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
O3BNTYR- 352.87165.91H-Bond
(Protein Donor)
O1ANSER- 373160.48H-Bond
(Protein Donor)
O1NNGLN- 382.9168.81H-Bond
(Protein Donor)
O7NNE2GLN- 383.06171.72H-Bond
(Protein Donor)
C3NCGGLN- 383.40Hydrophobic
O2BNH2ARG- 583.14146.5H-Bond
(Protein Donor)
O1XNH2ARG- 583.32140.66H-Bond
(Protein Donor)
DuArCZARG- 583.49178.85Pi/Cation
O1XOGSER- 612.68166.93H-Bond
(Protein Donor)
O2XOGSER- 632.5158.23H-Bond
(Protein Donor)
C4DCD2LEU- 903.850Hydrophobic
C1BCG1VAL- 913.840Hydrophobic
O3DOD1ASP- 932.65161.13H-Bond
(Ligand Donor)
O2DOD2ASP- 932.7163.2H-Bond
(Ligand Donor)
O3DNE2GLN- 963.11137.07H-Bond
(Protein Donor)
C2DCBHIS- 1184.170Hydrophobic
O7NNGLY- 1442.86135.27H-Bond
(Protein Donor)
N7NOSER- 2602.9164.29H-Bond
(Ligand Donor)
C2DCBSER- 2624.060Hydrophobic
O3DOHOH- 5012.8179.98H-Bond
(Protein Donor)
O1NOHOH- 5072.74161.65H-Bond
(Protein Donor)
O1XOHOH- 5312.79179.95H-Bond
(Protein Donor)