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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:

2y6q

2.370 Å

X-ray

2011-01-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:TetX family tetracycline inactivation enzyme
ID:Q93L51_BACT4
AC:Q93L51
Organism:Bacteroides thetaiotaomicron
Reign:Bacteria
TaxID:818
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:55.342
Number of residues:32
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0341117.125

% Hydrophobic% Polar
45.9254.08
According to VolSite

Ligand :
2y6q_4 Structure
HET Code: I7T
Formula: C21H19IN2O7
Molecular weight: 538.289 g/mol
DrugBank ID: -
Buried Surface Area:57.83 %
Polar Surface area: 171.08 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 3
Rings: 4
Aromatic rings: 1
Anionic atoms: 3
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 2

Mass center Coordinates

XYZ
0.937258-32.715914.4845


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
O3NE2GLN- 1923.32171.9H-Bond
(Protein Donor)
C6CEMET- 2153.950Hydrophobic
C61CEMET- 2154.180Hydrophobic
C5CD2PHE- 2243.510Hydrophobic
C41CGPHE- 2244.410Hydrophobic
C6CE2PHE- 2243.810Hydrophobic
I7SDMET- 3753.710Hydrophobic
I7CE1PHE- 3824.050Hydrophobic
O1CO4FAD- 13843.13173.49H-Bond
(Ligand Donor)