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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:

4c72

1.500 Å

X-ray

2013-09-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-oxoacyl-ACP synthase
ID:I6Y8T4_MYCTU
AC:I6Y8T4
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:16.353
Number of residues:34
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.324425.250

% Hydrophobic% Polar
59.5240.48
According to VolSite

Ligand :
4c72_1 Structure
HET Code: TLG
Formula: C12H13O3S
Molecular weight: 237.295 g/mol
DrugBank ID: -
Buried Surface Area:74.91 %
Polar Surface area: 82.5 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 0
Rings: 1
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-6.469-21.68227.435


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
C14CBALA- 2154.090Hydrophobic
C14CD2PHE- 2373.720Hydrophobic
C1CBPRO- 2803.940Hydrophobic
C3CGPRO- 2803.930Hydrophobic
O11NE2HIS- 3112.85173.28H-Bond
(Protein Donor)
C14CG2THR- 3153.920Hydrophobic
O11NE2HIS- 3452.99165.1H-Bond
(Protein Donor)
SCBPHE- 4023.960Hydrophobic
C1CBPHE- 4023.640Hydrophobic
C4CE1PHE- 4044.320Hydrophobic
C14CE1PHE- 4043.930Hydrophobic