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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:

4bkq

2.300 Å

X-ray

2013-04-29

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Enoyl-[acyl-carrier-protein] reductase [NADH]
ID:FABV_YERPE
AC:Q8Z9U1
Organism:Yersinia pestis
Reign:Bacteria
TaxID:632
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:58.241
Number of residues:55
Including
Standard Amino Acids: 54
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.5571107.000

% Hydrophobic% Polar
50.9149.09
According to VolSite

Ligand :
4bkq_1 Structure
HET Code: NAI
Formula: C21H27N7O14P2
Molecular weight: 663.425 g/mol
DrugBank ID: DB00157
Buried Surface Area:74.17 %
Polar Surface area: 342.9 Å2
Number of
H-Bond Acceptors: 19
H-Bond Donors: 6
Rings: 5
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
13.5859-23.7692-8.18666


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
O3BNSER- 733.15151.84H-Bond
(Protein Donor)
O3BOGSER- 732.68175.22H-Bond
(Ligand Donor)
O1AOG1THR- 742.75167.86H-Bond
(Protein Donor)
O1NNTYR- 762.83162.48H-Bond
(Protein Donor)
C4NCE2TYR- 763.730Hydrophobic
O2BNPHE- 973.47164.99H-Bond
(Protein Donor)
O2BOE2GLU- 982.87159.82H-Bond
(Ligand Donor)
N6AOD1ASP- 1342.91170.86H-Bond
(Ligand Donor)
N1ANALA- 1352.85167.46H-Bond
(Protein Donor)
C5DCBSER- 1614.490Hydrophobic
C1BCD2LEU- 1623.890Hydrophobic
C5DCBALA- 1634.150Hydrophobic
C3DCBALA- 1634.220Hydrophobic
C5BCBALA- 1634.030Hydrophobic
C3DCEMET- 2194.260Hydrophobic
C4DCBPHE- 2464.060Hydrophobic
C1DCBPHE- 2463.930Hydrophobic
C6NCBPHE- 2464.420Hydrophobic
C5NCBTYR- 2483.40Hydrophobic
O3DNZLYS- 2672.84127.45H-Bond
(Protein Donor)
O2DNZLYS- 2673.12137.3H-Bond
(Protein Donor)
C5NCBLEU- 2943.820Hydrophobic
O7NNVAL- 2972.89165.26H-Bond
(Protein Donor)
O2NOG1THR- 2992.6144.63H-Bond
(Protein Donor)