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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:

3mes

2.350 Å

X-ray

2010-03-31

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Putative choline kinase
ID:Q5CUP2_CRYPI
AC:Q5CUP2
Organism:Cryptosporidium parvum
Reign:Eukaryota
TaxID:353152
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:21.801
Number of residues:20
Including
Standard Amino Acids: 16
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors: ADP
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.564641.250

% Hydrophobic% Polar
35.7964.21
According to VolSite

Ligand :
3mes_1 Structure
HET Code: PT3
Formula: C7H12NO5
Molecular weight: 190.174 g/mol
DrugBank ID: DB03390
Buried Surface Area:54.68 %
Polar Surface area: 109.69 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 0
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
13.95452.7904637.5922


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
C42CBASN- 2724.110Hydrophobic
O1OHTYR- 2883.03149.51H-Bond
(Protein Donor)
C2CE2TYR- 2884.050Hydrophobic
C43CD2TYR- 3094.110Hydrophobic
O2MG MG- 4262.270Metal Acceptor