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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:

3phc

2.000 Å

X-ray

2010-11-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Purine nucleoside phosphorylase
ID:Q8I3X4_PLAF7
AC:Q8I3X4
Organism:Plasmodium falciparum
Reign:Eukaryota
TaxID:36329
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A86 %
B14 %


Ligand binding site composition:

B-Factor:30.735
Number of residues:37
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.409675.000

% Hydrophobic% Polar
39.0061.00
According to VolSite

Ligand :
3phc_1 Structure
HET Code: IM5
Formula: C12H18N5O3
Molecular weight: 280.303 g/mol
DrugBank ID: -
Buried Surface Area:74.28 %
Polar Surface area: 128.17 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 6
Rings: 3
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 3

Mass center Coordinates

XYZ
-16.79179.76185-18.9069


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
O5'NE2HIS- 72.54163.49H-Bond
(Protein Donor)
C3'CG1VAL- 663.780Hydrophobic
C4'CG2VAL- 664.310Hydrophobic
C5'CG1VAL- 664.250Hydrophobic
C5'CE1TYR- 1603.90Hydrophobic
C3'SDMET- 1833.680Hydrophobic
C5'SDMET- 1834.20Hydrophobic
O3'OE2GLU- 1842.66148.99H-Bond
(Ligand Donor)
N7OD1ASP- 2062.83151.32H-Bond
(Ligand Donor)
O6OHOH- 2812.76165.1H-Bond
(Protein Donor)