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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:

4mqy

2.000 Å

X-ray

2013-09-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UDP-3-O-acyl-N-acetylglucosamine deacetylase
ID:LPXC_ECOLI
AC:P0A725
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:47.172
Number of residues:38
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
1.034590.625

% Hydrophobic% Polar
48.0052.00
According to VolSite

Ligand :
4mqy_1 Structure
HET Code: 2CW
Formula: C22H19N3O4
Molecular weight: 389.404 g/mol
DrugBank ID: -
Buried Surface Area:63.34 %
Polar Surface area: 121.84 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 3
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
192.119101.3095.04203


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
C09CD2LEU- 183.670Hydrophobic
C24CD2LEU- 624.350Hydrophobic
C09CG2THR- 1913.820Hydrophobic
C28CZPHE- 1923.760Hydrophobic
C18CEMET- 1953.810Hydrophobic
C13CD1ILE- 1983.260Hydrophobic
C21CG2ILE- 1983.460Hydrophobic
C12CD1ILE- 1983.610Hydrophobic
C12SGCYS- 2074.440Hydrophobic
C12CBALA- 2153.690Hydrophobic
C14CG2VAL- 2174.030Hydrophobic
C17CG2VAL- 2173.920Hydrophobic
O04NE2HIS- 2652.86147.57H-Bond
(Protein Donor)
O01ZN ZN- 4012.410Metal Acceptor
O04ZN ZN- 4011.980Metal Acceptor