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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:

3nzk

1.800 Å

X-ray

2010-07-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:UDP-3-O-acyl-N-acetylglucosamine deacetylase
ID:A1JJJ9_YERE8
AC:A1JJJ9
Organism:Yersinia enterocolitica serotype O:8 / biotype 1B
Reign:Bacteria
TaxID:393305
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:20.777
Number of residues:38
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
1.029870.750

% Hydrophobic% Polar
53.1046.90
According to VolSite

Ligand :
3nzk_2 Structure
HET Code: C90
Formula: C24H28N3O5
Molecular weight: 438.496 g/mol
DrugBank ID: DB07536
Buried Surface Area:55.75 %
Polar Surface area: 112.33 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-21.9655-17.4928-34.683


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
C11CD1LEU- 184.290Hydrophobic
CF1CD2LEU- 1840Hydrophobic
N17OG1THR- 1912.97149.43H-Bond
(Ligand Donor)
CF1CG2THR- 1914.030Hydrophobic
C21CE2PHE- 1924.020Hydrophobic
CA1SDMET- 1953.710Hydrophobic
C9CD1ILE- 1983.930Hydrophobic
C10CG1ILE- 1983.760Hydrophobic
CE2CG1ILE- 1983.990Hydrophobic
CD1CG2ILE- 1983.660Hydrophobic
CFCD1LEU- 2013.990Hydrophobic
CD1CBCYS- 2074.40Hydrophobic
CE2SGCYS- 2073.60Hydrophobic
CA1CZPHE- 2123.710Hydrophobic
CA2CE2PHE- 2124.390Hydrophobic
CD2CBALA- 2154.330Hydrophobic
CE1CBALA- 2153.840Hydrophobic
C11CBALA- 2154.30Hydrophobic
CD2CG2VAL- 2173.380Hydrophobic
O22ZN ZN- 3072.10Metal Acceptor
O24ZN ZN- 3072.280Metal Acceptor