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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:

1ig0

1.800 Å

X-ray

2001-04-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Thiamine pyrophosphokinase
ID:THI80_YEAST
AC:P35202
Organism:Saccharomyces cerevisiae
Reign:Eukaryota
TaxID:559292
EC Number:2.7.6.2


Chains:

Chain Name:Percentage of Residues
within binding site
A46 %
B54 %


Ligand binding site composition:

B-Factor:23.092
Number of residues:27
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.365550.125

% Hydrophobic% Polar
23.9376.07
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median1ig0HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
1ig0_1 Structure
HET Code: VIB
Formula: C12H17N4OS
Molecular weight: 265.355 g/mol
DrugBank ID: DB00152
Buried Surface Area:66.19 %
Polar Surface area: 104.15 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
47.449830.916422.4067
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median1ig0RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


Binding mode :
What is Poseview ?
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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
CM2SGCYS- 53.980Hydrophobic
N4AOGLN- 1222.98150.79H-Bond
(Ligand Donor)
CM4CBGLN- 1224.110Hydrophobic
S1CG2THR- 1253.820Hydrophobic
CM2CBTRP- 2704.20Hydrophobic
CM4CH2TRP- 2703.60Hydrophobic
C5ACBTRP- 2704.230Hydrophobic
CM2CG1VAL- 2723.70Hydrophobic
CM2CZ2TRP- 2753.730Hydrophobic
CM2CBSER- 2854.140Hydrophobic
N1AOGSER- 2852.67168.65H-Bond
(Protein Donor)
CM4CBSER- 2873.730Hydrophobic
C7CBSER- 2873.820Hydrophobic
O1OGSER- 2873.42166.82H-Bond
(Protein Donor)
O1OHOH- 10112.97162.17H-Bond
(Protein Donor)