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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:

1y1r

2.110 Å

X-ray

2004-11-19

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
B15 %
D85 %


Ligand binding site composition:

B-Factor:22.015
Number of residues:26
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.327698.625

% Hydrophobic% Polar
48.7951.21
According to VolSite

Ligand :
1y1r_2 Structure
HET Code: ANU
Formula: C9H10N2O5
Molecular weight: 226.186 g/mol
DrugBank ID: DB04627
Buried Surface Area:71.6 %
Polar Surface area: 91.59 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 2
Rings: 3
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
-6.4772547.660888.4249


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
C5'CG1ILE- 30694.080Hydrophobic
N3NE2GLN- 31663.03129.02H-Bond
(Protein Donor)
O4NH1ARG- 31683.25125.41H-Bond
(Protein Donor)
C1'CBGLU- 31964.370Hydrophobic
O3'NMET- 31973.03158.45H-Bond
(Protein Donor)
C3'CBMET- 31973.560Hydrophobic
C2'CGMET- 31973.520Hydrophobic
C5'SDMET- 31974.150Hydrophobic
O3'OE1GLU- 31983.4129.36H-Bond
(Ligand Donor)