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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:

4giu

1.670 Å

X-ray

2012-08-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Anthranilate phosphoribosyltransferase
ID:TRPD_MYCTU
AC:P9WFX5
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:16.455
Number of residues:32
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.753914.625

% Hydrophobic% Polar
40.5959.41
According to VolSite

Ligand :
4giu_1 Structure
HET Code: 636
Formula: C16H13NO4
Molecular weight: 283.279 g/mol
DrugBank ID: -
Buried Surface Area:62.18 %
Polar Surface area: 92.29 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
2.32748-28.300933.6517


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
CX4CEMET- 864.450Hydrophobic
C3CEMET- 864.080Hydrophobic
C5CG2VAL- 1064.280Hydrophobic
OX1ND2ASN- 1382.82154.78H-Bond
(Protein Donor)
CY5CBASN- 1383.90Hydrophobic
CX3CBALA- 1793.630Hydrophobic
CY6CBALA- 1793.820Hydrophobic
CX4CBALA- 1793.410Hydrophobic
CX6CGPRO- 1804.170Hydrophobic
CX4CBHIS- 1833.650Hydrophobic
C3CE2TYR- 1864.160Hydrophobic
CX4CD2TYR- 1863.50Hydrophobic
CX5CBTYR- 1864.280Hydrophobic
OX2NH1ARG- 1933.28135.24H-Bond
(Protein Donor)
OY1NH1ARG- 1933.07140.92H-Bond
(Protein Donor)
OY1NH2ARG- 1932.88152.27H-Bond
(Protein Donor)
OY2NH2ARG- 1933.38143.49H-Bond
(Protein Donor)
OY1CZARG- 1933.40Ionic
(Protein Cationic)
OY2OHOH- 5202.8179.97H-Bond
(Protein Donor)