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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:

4ogk

2.400 Å

X-ray

2014-01-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uridine phosphorylase
ID:UDP_SALTY
AC:P0A1F6
Organism:Salmonella typhimurium
Reign:Bacteria
TaxID:99287
EC Number:2.4.2.3


Chains:

Chain Name:Percentage of Residues
within binding site
E90 %
F10 %


Ligand binding site composition:

B-Factor:59.258
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9541447.875

% Hydrophobic% Polar
39.8660.14
According to VolSite

Ligand :
4ogk_4 Structure
HET Code: THM
Formula: C10H14N2O5
Molecular weight: 242.229 g/mol
DrugBank ID: DB04485
Buried Surface Area:69.5 %
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
-53.118158.38551.91329


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
C3'CG1ILE- 694.140Hydrophobic
O5'NH2ARG- 913.06132.92H-Bond
(Protein Donor)
C5MCG2THR- 944.460Hydrophobic
C2'CE2PHE- 1624.020Hydrophobic
N3OE1GLN- 1662.87125.21H-Bond
(Ligand Donor)
C4'CBGLU- 1964.340Hydrophobic
C2'SDMET- 1973.980Hydrophobic
C1'CGMET- 1974.060Hydrophobic
O5'OE1GLU- 1982.56133.82H-Bond
(Ligand Donor)
O3'OE1GLU- 1983.24168.33H-Bond
(Ligand Donor)
C5MCD1ILE- 2203.430Hydrophobic
C5MCG1VAL- 2213.990Hydrophobic