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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:

3djf

2.300 Å

X-ray

2008-06-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Purine nucleoside phosphorylase
ID:Q9BMI9_SCHMA
AC:Q9BMI9
Organism:Schistosoma mansoni
Reign:Eukaryota
TaxID:6183
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A97 %
B3 %


Ligand binding site composition:

B-Factor:35.477
Number of residues:31
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.093448.875

% Hydrophobic% Polar
57.8942.11
According to VolSite

Ligand :
3djf_1 Structure
HET Code: BC3
Formula: C12H11N5O
Molecular weight: 241.249 g/mol
DrugBank ID: DB02568
Buried Surface Area:69.94 %
Polar Surface area: 96.16 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
-18.0807-2.5934428.5311


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
C06CBALA- 1184.130Hydrophobic
N01OE2GLU- 2032.68173.55H-Bond
(Ligand Donor)
N18OE1GLU- 2032.8170.44H-Bond
(Ligand Donor)
C08CEMET- 2213.690Hydrophobic
N14OD1ASN- 2452.85172.46H-Bond
(Ligand Donor)
O17ND2ASN- 2452.97177.6H-Bond
(Protein Donor)