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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:

4yek

2.550 Å

X-ray

2015-02-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Thymidine phosphorylase
ID:TYPH_SALTY
AC:Q7CP66
Organism:Salmonella typhimurium
Reign:Bacteria
TaxID:99287
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:68.578
Number of residues:20
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1111039.500

% Hydrophobic% Polar
40.9159.09
According to VolSite

Ligand :
4yek_1 Structure
HET Code: THM
Formula: C10H14N2O5
Molecular weight: 242.229 g/mol
DrugBank ID: DB04485
Buried Surface Area:48.31 %
Polar Surface area: 99.1 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
217.12752.10085.66971


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
O3'OTHR- 873.12165.48H-Bond
(Ligand Donor)
C5MCE1TYR- 1684.110Hydrophobic
O4NH2ARG- 1713.13141.75H-Bond
(Protein Donor)
O4NH1ARG- 1713.11143.06H-Bond
(Protein Donor)
C5MCG1VAL- 1773.340Hydrophobic
C5MCG1ILE- 1833.770Hydrophobic
N3OGSER- 1863.04145.82H-Bond
(Ligand Donor)
C3'CD2PHE- 2104.30Hydrophobic
C2'CE2PHE- 2103.740Hydrophobic
C5MCZPHE- 2103.750Hydrophobic