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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:

1odi

2.400 Å

X-ray

2003-02-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Purine nucleoside phosphorylase
ID:Q5SID9_THET8
AC:Q5SID9
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:300852
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C88 %
D12 %


Ligand binding site composition:

B-Factor:29.875
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.643958.500

% Hydrophobic% Polar
37.6862.32
According to VolSite

Ligand :
1odi_3 Structure
HET Code: ADN
Formula: C10H13N5O4
Molecular weight: 267.241 g/mol
DrugBank ID: DB00640
Buried Surface Area:75.09 %
Polar Surface area: 139.54 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
7.06126-122.953-139.361


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
C4'SDMET- 653.960Hydrophobic
C5'CE1PHE- 1593.610Hydrophobic
C2'CBGLU- 1794.150Hydrophobic
C2'CGMET- 1804.010Hydrophobic
C3'SDMET- 1803.520Hydrophobic
O2'NMET- 1803.08152.16H-Bond
(Protein Donor)
O3'OE1GLU- 1812.52172.25H-Bond
(Protein Donor)
N7ND2ASN- 2043.1163.85H-Bond
(Protein Donor)
N6OD1ASN- 2043.28156.97H-Bond
(Ligand Donor)