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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:

3img

1.800 Å

X-ray

2009-08-10

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pantothenate synthetase
ID:PANC_MYCTU
AC:P9WIL5
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:6.3.2.1


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:23.957
Number of residues:23
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.884928.125

% Hydrophobic% Polar
43.6456.36
According to VolSite

Ligand :
3img_3 Structure
HET Code: BZ2
Formula: C9H5O3
Molecular weight: 161.134 g/mol
DrugBank ID: -
Buried Surface Area:51.85 %
Polar Surface area: 53.27 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 0
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
2.06508-10.671331.5293


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
CAECBPRO- 383.880Hydrophobic
OAANMET- 402.91154.61H-Bond
(Protein Donor)
CAKCGMET- 403.760Hydrophobic
OAANE2HIS- 472.76155.59H-Bond
(Protein Donor)
CADCG1VAL- 1393.780Hydrophobic
CACCG1VAL- 14240Hydrophobic
CADCG2VAL- 1433.520Hydrophobic
OABOHOH- 6333.3179.97H-Bond
(Protein Donor)