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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:

3o8g

1.900 Å

X-ray

2010-08-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:HTH-type transcriptional regulator EthR
ID:ETHR_MYCTU
AC:P9WMC1
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:13.739
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.655472.500

% Hydrophobic% Polar
65.7134.29
According to VolSite

Ligand :
3o8g_1 Structure
HET Code: O8G
Formula: C13H14N6O2S
Molecular weight: 318.354 g/mol
DrugBank ID: -
Buried Surface Area:71.93 %
Polar Surface area: 137.22 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 0
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
32.751471.631611.8924


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
C11CD2LEU- 873.950Hydrophobic
C1CG1ILE- 1074.070Hydrophobic
C11CE1PHE- 1103.760Hydrophobic
S33CG2VAL- 1524.110Hydrophobic
O17ND2ASN- 1792.97174.97H-Bond
(Protein Donor)
C14CH2TRP- 2073.980Hydrophobic