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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:

4gee

1.700 Å

X-ray

2012-08-01

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:DNA gyrase subunit B
ID:GYRB_ENTFA
AC:Q839Z1
Organism:Enterococcus faecalis
Reign:Bacteria
TaxID:226185
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:16.097
Number of residues:28
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.578239.625

% Hydrophobic% Polar
52.1147.89
According to VolSite

Ligand :
4gee_1 Structure
HET Code: 0WT
Formula: C17H19ClN7O
Molecular weight: 372.832 g/mol
DrugBank ID: -
Buried Surface Area:62.68 %
Polar Surface area: 107.46 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 2
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-10.2403-4.85015-14.7652


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
C10CG2ILE- 453.740Hydrophobic
CL1CBASN- 483.530Hydrophobic
C3CBASN- 483.870Hydrophobic
C14CBASN- 484.120Hydrophobic
C21CGGLU- 524.420Hydrophobic
C11CG1VAL- 734.080Hydrophobic
N1OD1ASP- 752.66167.59H-Bond
(Ligand Donor)
DuArCZARG- 783.82157.27Pi/Cation
CL1CD1ILE- 803.960Hydrophobic
C3CG1ILE- 803.470Hydrophobic
C17CG2ILE- 804.030Hydrophobic
C14CD1ILE- 804.360Hydrophobic
C16CG2VAL- 963.990Hydrophobic
C14CG1VAL- 963.840Hydrophobic
CL1CZPHE- 974.370Hydrophobic
N19OGLY- 1193.08162.95H-Bond
(Ligand Donor)
CL1CBSER- 1224.490Hydrophobic
C11CG2THR- 1673.770Hydrophobic
C11CG2VAL- 1693.830Hydrophobic
N9OHOH- 4072.83179.97H-Bond
(Protein Donor)