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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:

3fi8

2.300 Å

X-ray

2008-12-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Choline kinase
ID:Q8IM71_PLAF7
AC:Q8IM71
Organism:Plasmodium falciparum
Reign:Eukaryota
TaxID:36329
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:27.920
Number of residues:19
Including
Standard Amino Acids: 16
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors: ADP
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.321685.125

% Hydrophobic% Polar
35.9664.04
According to VolSite

Ligand :
3fi8_1 Structure
HET Code: OPE
Formula: C2H7NO4P
Molecular weight: 140.055 g/mol
DrugBank ID: DB01738
Buried Surface Area:55.62 %
Polar Surface area: 109.87 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 1
Rings: 0
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
8.21755.5623810.9594


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
NOD2ASP- 2882.68171.74H-Bond
(Ligand Donor)
NOD2ASP- 2882.680Ionic
(Ligand Cationic)
O3NE2GLN- 2902.71127.9H-Bond
(Protein Donor)
NOD2ASP- 3053.970Ionic
(Ligand Cationic)
CACH2TRP- 3953.610Hydrophobic
O2OHOH- 4562.73163.33H-Bond
(Protein Donor)