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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:

2x9d

2.340 Å

X-ray

2010-03-15

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:43.392
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.427745.875

% Hydrophobic% Polar
50.6849.32
According to VolSite

Ligand :
2x9d_1 Structure
HET Code: ITC
Formula: C22H22ClN2O8
Molecular weight: 477.872 g/mol
DrugBank ID: -
Buried Surface Area:59.51 %
Polar Surface area: 174.31 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 4
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
21.675836.772234.4675


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
O3NE2HIS- 643.18164.5H-Bond
(Protein Donor)
O3ND2ASN- 822.93155.21H-Bond
(Protein Donor)
N4OD1ASN- 822.65139.62H-Bond
(Ligand Donor)
C10CDARG- 1043.960Hydrophobic
C6BCGPRO- 1054.390Hydrophobic
C5BCGPRO- 1054.410Hydrophobic
O3NE2GLN- 1163.15122.23H-Bond
(Protein Donor)
C6'CD1LEU- 1314.250Hydrophobic
C5CG2ILE- 1344.10Hydrophobic
C6'CG2ILE- 1343.490Hydrophobic
CL7CBSER- 1354.130Hydrophobic
C4ACBSER- 1384.290Hydrophobic
C5ACBSER- 1384.380Hydrophobic
CL7CBSER- 1383.650Hydrophobic