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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:

4ddh

2.070 Å

X-ray

2012-01-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pantothenate synthetase
ID:PANC_MYCTO
AC:P9WIL4
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83331
EC Number:6.3.2.1


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:25.866
Number of residues:25
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.558894.375

% Hydrophobic% Polar
40.0060.00
According to VolSite

Ligand :
4ddh_2 Structure
HET Code: MS0
Formula: C11H9O4
Molecular weight: 205.187 g/mol
DrugBank ID: -
Buried Surface Area:67.89 %
Polar Surface area: 62.5 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 0
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
0.282333-10.318939.4561


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
O11NE2HIS- 442.91173.6H-Bond
(Protein Donor)
C19CD2LEU- 504.290Hydrophobic
C22CD2LEU- 504.090Hydrophobic
O12NZLYS- 1602.76146.75H-Bond
(Protein Donor)
O12NZLYS- 1602.760Ionic
(Protein Cationic)
C16CBLYS- 1603.840Hydrophobic
O21NVAL- 1872.94174.66H-Bond
(Protein Donor)
C22CG2VAL- 1873.820Hydrophobic
C16CBMET- 1954.110Hydrophobic
O11NSER- 1973.19168.77H-Bond
(Protein Donor)