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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:

2x0f

2.550 Å

X-ray

2009-12-08

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:WsaF
ID:Q7BG50_GEOSE
AC:Q7BG50
Organism:Geobacillus stearothermophilus
Reign:Bacteria
TaxID:1422
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:37.337
Number of residues:34
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9621383.750

% Hydrophobic% Polar
43.9056.10
According to VolSite

Ligand :
2x0f_1 Structure
HET Code: TRH
Formula: C16H24N2O15P2
Molecular weight: 546.314 g/mol
DrugBank ID: DB03723
Buried Surface Area:54.8 %
Polar Surface area: 276.36 Å2
Number of
H-Bond Acceptors: 15
H-Bond Donors: 5
Rings: 3
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-10.1716.88-12.9797


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
O4OLYS- 2253.29168.79H-Bond
(Ligand Donor)
C5ACE1TYR- 2473.890Hydrophobic
C5ACG2VAL- 2823.720Hydrophobic
N31OLEU- 3032.82163.66H-Bond
(Ligand Donor)
O41NLEU- 3033.03149.82H-Bond
(Protein Donor)
C1'CD2LEU- 3053.640Hydrophobic
C5ACE1TYR- 3083.610Hydrophobic
C2'CE2TYR- 3083.730Hydrophobic
C1CE2TYR- 3294.180Hydrophobic
C2CD1TYR- 3293.820Hydrophobic
C3CE1TYR- 3293.670Hydrophobic