Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4a6n

2.300 Å

X-ray

2011-11-07

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
A100 %


Ligand binding site composition:

B-Factor:59.498
Number of residues:34
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.667482.625

% Hydrophobic% Polar
47.5552.45
According to VolSite

Ligand :
4a6n_1 Structure
HET Code: T1C
Formula: C29H38N5O8
Molecular weight: 584.641 g/mol
DrugBank ID: -
Buried Surface Area:48.12 %
Polar Surface area: 220.02 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 5
Rings: 4
Aromatic rings: 1
Anionic atoms: 3
Cationic atoms: 2
Rule of Five Violation: 2
Rotatable Bonds: 7

Mass center Coordinates

XYZ
-0.47338110.408223.2039


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
O1NH2ARG- 2133.17169H-Bond
(Protein Donor)
C71SDMET- 2154.060Hydrophobic
C6SDMET- 2154.440Hydrophobic
C71CE1PHE- 2244.30Hydrophobic
C5CE1PHE- 2243.250Hydrophobic
C41CGPHE- 2244.390Hydrophobic
C6CE1PHE- 2243.560Hydrophobic
N92OE2GLU- 3673.44134.87H-Bond
(Ligand Donor)
N92OE2GLU- 3673.440Ionic
(Ligand Cationic)
C71SDMET- 3753.840Hydrophobic
C72SDMET- 3753.290Hydrophobic
C71CE1PHE- 3823.390Hydrophobic
O1CO4FAD- 3892.84152.86H-Bond
(Ligand Donor)