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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:

4u95

2.000 Å

X-ray

2014-08-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Multidrug efflux pump subunit AcrB
ID:ACRB_ECOLI
AC:P31224
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:36.127
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.7791765.125

% Hydrophobic% Polar
51.6348.37
According to VolSite

Ligand :
4u95_1 Structure
HET Code: MIY
Formula: C23H25N3O7
Molecular weight: 455.460 g/mol
DrugBank ID: DB01017
Buried Surface Area:42.33 %
Polar Surface area: 174.32 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 4
Aromatic rings: 1
Anionic atoms: 3
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
35.6663-61.1675-41.9241


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
C71CE1PHE- 1783.550Hydrophobic
C13CBPHE- 1783.610Hydrophobic
O7OD1ASN- 2742.82163.25H-Bond
(Ligand Donor)
C8CG1ILE- 2774.370Hydrophobic
C13CG2ILE- 2773.50Hydrophobic
C12CBALA- 2793.930Hydrophobic
C11CG1VAL- 6123.890Hydrophobic
CN7CD1PHE- 6153.220Hydrophobic