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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:

3tp0

1.900 Å

X-ray

2011-09-07

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:21.675
Number of residues:31
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.595408.375

% Hydrophobic% Polar
66.9433.06
According to VolSite

Ligand :
3tp0_1 Structure
HET Code: FO5
Formula: C14H14N4O2S
Molecular weight: 302.352 g/mol
DrugBank ID: -
Buried Surface Area:69.59 %
Polar Surface area: 111.26 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 0
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-7.84829-26.58543.48476


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
C6CD2LEU- 874.070Hydrophobic
SCD2LEU- 904.090Hydrophobic
SCGMET- 1024.130Hydrophobic
C5CZ3TRP- 1034.350Hydrophobic
C4CG1ILE- 1074.220Hydrophobic
C1CGPHE- 1103.590Hydrophobic
C4CE2PHE- 1104.240Hydrophobic
C6CE2PHE- 1103.770Hydrophobic
C1CE3TRP- 1454.120Hydrophobic
OND2ASN- 1792.79176.42H-Bond
(Protein Donor)
C5CH2TRP- 2073.950Hydrophobic