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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:

4ac0

2.450 Å

X-ray

2011-12-12

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Tetracycline repressor protein class B from transposon Tn10
ID:TETR2_ECOLX
AC:P04483
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:57.544
Number of residues:31
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.903742.500

% Hydrophobic% Polar
48.1851.82
According to VolSite

Ligand :
4ac0_1 Structure
HET Code: MIY
Formula: C23H25N3O7
Molecular weight: 455.460 g/mol
DrugBank ID: DB01017
Buried Surface Area:50.33 %
Polar Surface area: 174.32 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 4
Aromatic rings: 1
Anionic atoms: 3
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
12.9546-0.0496061-9.86576


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
O2ND2ASN- 823.07158.65H-Bond
(Protein Donor)
N1OD1ASN- 822.61147.39H-Bond
(Ligand Donor)
C14CGPRO- 1053.940Hydrophobic
C6CD2LEU- 1133.630Hydrophobic
O8NE2GLN- 1163.21151.4H-Bond
(Protein Donor)
O2NE2GLN- 1162.7144.49H-Bond
(Protein Donor)
CN7CD2LEU- 1314.50Hydrophobic
C71CD2LEU- 1313.870Hydrophobic
CN7CBLEU- 1344.490Hydrophobic
O6MG MG- 12051.970Metal Acceptor
O5MG MG- 12051.990Metal Acceptor