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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:

4fex

2.710 Å

X-ray

2012-05-30

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aminoglycoside 3'-phosphotransferase AphA1-IAB
ID:B0VD92_ACIBY
AC:B0VD92
Organism:Acinetobacter baumannii
Reign:Bacteria
TaxID:509173
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A96 %
B4 %


Ligand binding site composition:

B-Factor:53.944
Number of residues:28
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.881715.500

% Hydrophobic% Polar
44.8155.19
According to VolSite

Ligand :
4fex_1 Structure
HET Code: 0TO
Formula: C16H14ClN3O2
Molecular weight: 315.754 g/mol
DrugBank ID: -
Buried Surface Area:58.79 %
Polar Surface area: 56.27 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-28.2024-59.914217.4258


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
C17CD1ILE- 403.60Hydrophobic
C7CBPHE- 534.370Hydrophobic
C19CGLYS- 553.540Hydrophobic
CLCD1LEU- 723.680Hydrophobic
CLCGPRO- 823.910Hydrophobic
CLCG2THR- 983.530Hydrophobic
N9NILE- 1013.06148.39H-Bond
(Protein Donor)
C14CG2THR- 1053.490Hydrophobic
C15CD1ILE- 2053.870Hydrophobic
C14CD1ILE- 2153.650Hydrophobic
C3CD1ILE- 2153.470Hydrophobic