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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:

5dro

2.010 Å

X-ray

2015-09-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UDP-3-O-acyl-N-acetylglucosamine deacetylase
ID:LPXC_AQUAE
AC:O67648
Organism:Aquifex aeolicus
Reign:Bacteria
TaxID:224324
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:18.282
Number of residues:34
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.366772.875

% Hydrophobic% Polar
45.4154.59
According to VolSite

Ligand :
5dro_1 Structure
HET Code: ZH2
Formula: C21H19N3O4
Molecular weight: 377.393 g/mol
DrugBank ID: -
Buried Surface Area:52.38 %
Polar Surface area: 124.68 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 5
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
-31.51467.5890719.4121


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
C11CG1ILE- 183.980Hydrophobic
N03OHIS- 583.48131.2H-Bond
(Ligand Donor)
C10CG2THR- 1794.350Hydrophobic
O01OG1THR- 1792.74143.19H-Bond
(Protein Donor)
N06OG1THR- 1793.06144.98H-Bond
(Ligand Donor)
C28CE1PHE- 1803.970Hydrophobic
C13CBALA- 1813.670Hydrophobic
C12CBALA- 1813.470Hydrophobic
C18CD1ILE- 1864.410Hydrophobic
C15CD1ILE- 1863.950Hydrophobic
C24CG1ILE- 1894.160Hydrophobic
C25CD1ILE- 1894.170Hydrophobic
C13CG2THR- 2033.940Hydrophobic
C11CG2THR- 2033.720Hydrophobic
O27NZLYS- 2273.17154.55H-Bond
(Protein Donor)
O27OD2ASP- 2302.96140.77H-Bond
(Ligand Donor)
O01ZN ZN- 4012.10Metal Acceptor
O04ZN ZN- 4012.180Metal Acceptor