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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:

4lcf

1.600 Å

X-ray

2013-06-21

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UDP-3-O-acyl-N-acetylglucosamine deacetylase
ID:LPXC_PSEAE
AC:P47205
Organism:Pseudomonas aeruginosa
Reign:Bacteria
TaxID:208964
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:20.769
Number of residues:35
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
1.150837.000

% Hydrophobic% Polar
51.6148.39
According to VolSite

Ligand :
4lcf_1 Structure
HET Code: 1WL
Formula: C23H19N5O3
Molecular weight: 413.429 g/mol
DrugBank ID: -
Buried Surface Area:49.57 %
Polar Surface area: 133.13 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 5
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
26.1762-15.055-6.03016


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
C12CD1LEU- 184.130Hydrophobic
C10CD2LEU- 183.980Hydrophobic
O01OG1THR- 1902.52125.4H-Bond
(Protein Donor)
N06OG1THR- 1902.92131H-Bond
(Ligand Donor)
C25CG2THR- 1903.960Hydrophobic
N28OPHE- 1912.79135.96H-Bond
(Ligand Donor)
C14CD1ILE- 1973.520Hydrophobic
C17CG2ILE- 1974.40Hydrophobic
C13CG1ILE- 1973.780Hydrophobic
C15CG2ILE- 1973.620Hydrophobic
C11CD1LEU- 2004.280Hydrophobic
C19CG1VAL- 2113.910Hydrophobic
C24CBALA- 2144.030Hydrophobic
C13CBALA- 2144.260Hydrophobic
C18CG2VAL- 2163.590Hydrophobic
O01ZN ZN- 3112.090Metal Acceptor
O04ZN ZN- 3112.260Metal Acceptor