Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1nw4

2.200 Å

X-ray

2003-02-05

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
C88 %
D12 %


Ligand binding site composition:

B-Factor:28.577
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.516823.500

% Hydrophobic% Polar
41.3958.61
According to VolSite

Ligand :
1nw4_3 Structure
HET Code: IMH
Formula: C11H15N4O4
Molecular weight: 267.261 g/mol
DrugBank ID: DB06185
Buried Surface Area:72.91 %
Polar Surface area: 139.1 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 2

Mass center Coordinates

XYZ
47.13449.85653113.992


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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- 72.68166.79H-Bond
(Ligand Donor)
C5'CG1VAL- 664.120Hydrophobic
C3'CG1VAL- 663.990Hydrophobic
N4'OGSER- 913.39120.52H-Bond
(Ligand Donor)
C5'CE1TYR- 1603.990Hydrophobic
C2'CBGLU- 1824.430Hydrophobic
C5'SDMET- 1834.30Hydrophobic
C3'SDMET- 1833.70Hydrophobic
C2'CGMET- 1833.760Hydrophobic
O2'NMET- 1832.83131.25H-Bond
(Protein Donor)
O3'OE2GLU- 1842.7156.13H-Bond
(Ligand Donor)
O2'OE1GLU- 1842.92136.3H-Bond
(Ligand Donor)
N7OD1ASP- 2062.9166.27H-Bond
(Ligand Donor)
O6OHOH- 8382.96179.96H-Bond
(Protein Donor)