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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:

4hz5

2.700 Å

X-ray

2012-11-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:DNA topoisomerase 4 subunit B
ID:PARE_ENTFA
AC:H7C794
Organism:Enterococcus faecalis
Reign:Bacteria
TaxID:226185
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C84 %
G16 %


Ligand binding site composition:

B-Factor:44.962
Number of residues:32
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.598438.750

% Hydrophobic% Polar
46.1553.85
According to VolSite

Ligand :
4hz5_3 Structure
HET Code: 19Y
Formula: C15H14N4O2S
Molecular weight: 314.362 g/mol
DrugBank ID: -
Buried Surface Area:67.68 %
Polar Surface area: 106.06 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
10.227439.452-5.90818


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
C21CG2ILE- 463.660Hydrophobic
C21CBASN- 494.110Hydrophobic
C4CBASN- 494.350Hydrophobic
C22CBALA- 504.120Hydrophobic
S10CGGLU- 533.910Hydrophobic
C22CG1VAL- 743.930Hydrophobic
N2OD2ASP- 762.75170.5H-Bond
(Ligand Donor)
S10CBARG- 794.50Hydrophobic
C4CGMET- 813.950Hydrophobic
C18CD1ILE- 963.810Hydrophobic
C22CG2THR- 1694.340Hydrophobic
C21CG2VAL- 1714.020Hydrophobic