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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:

2go4

2.700 Å

X-ray

2006-04-12

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
A15 %
B85 %


Ligand binding site composition:

B-Factor:53.990
Number of residues:48
Including
Standard Amino Acids: 45
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors:
Metals: ZN

Cavity properties

LigandabilityVolume (Å3)
0.9821549.125

% Hydrophobic% Polar
48.5851.42
According to VolSite

Ligand :
2go4_2 Structure
HET Code: TUX
Formula: C22H41NO7
Molecular weight: 431.563 g/mol
DrugBank ID: DB01991
Buried Surface Area:59.69 %
Polar Surface area: 125.32 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 4
Rings: 1
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 17

Mass center Coordinates

XYZ
-40.077167.041325.9453


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
C4ACD1ILE- 183.510Hydrophobic
C3GCBHIS- 584.430Hydrophobic
O4GND1HIS- 583.07157.92H-Bond
(Protein Donor)
C2ACG2THR- 1914.350Hydrophobic
CZHCG2THR- 1913.760Hydrophobic
C2ACBALA- 1934.080Hydrophobic
O4GOE2GLU- 1973.34161.95H-Bond
(Ligand Donor)
C9ACD1ILE- 1983.830Hydrophobic
C2ACD1ILE- 2014.080Hydrophobic
CDACBSER- 2113.230Hydrophobic
CAACD2LEU- 2123.830Hydrophobic
CCACGLEU- 2123.780Hydrophobic
CEACGLEU- 2123.810Hydrophobic
C5ACG2THR- 2154.410Hydrophobic
C6ACBTHR- 2154.150Hydrophobic
C9ACG2VAL- 2174.150Hydrophobic
O5GNZLYS- 2393.42120.03H-Bond
(Protein Donor)
OYHZN ZN- 6022.110Metal Acceptor
OXHZN ZN- 6021.890Metal Acceptor