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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:

2vke

1.620 Å

X-ray

2007-12-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Tetracycline repressor protein class D
ID:TETR4_ECOLX
AC:P0ACT4
Organism:Escherichia coli
Reign:Bacteria
TaxID:562
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:27.836
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.184762.750

% Hydrophobic% Polar
43.8156.19
According to VolSite

Ligand :
2vke_1 Structure
HET Code: TAC
Formula: C22H22N2O8
Molecular weight: 442.419 g/mol
DrugBank ID: DB00759
Buried Surface Area:57.57 %
Polar Surface area: 191.3 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 4
Rings: 4
Aromatic rings: 1
Anionic atoms: 3
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
19.961235.10534.8101


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
O3ND2ASN- 822.71158.57H-Bond
(Protein Donor)
N4OD1ASN- 822.6150.35H-Bond
(Ligand Donor)
C9CDARG- 1043.680Hydrophobic
C1ACGPRO- 1053.710Hydrophobic
C62CBVAL- 1134.160Hydrophobic
O21NE2GLN- 1163.15146.53H-Bond
(Protein Donor)
O3NE2GLN- 1163.19140.06H-Bond
(Protein Donor)
C62CGLEU- 1174.260Hydrophobic
C7CD1LEU- 1314.270Hydrophobic
C62CG2ILE- 1343.990Hydrophobic
C5CG2ILE- 1343.780Hydrophobic