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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:

3zm9

1.900 Å

X-ray

2013-02-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Choline kinase alpha
ID:CHKA_HUMAN
AC:P35790
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.1.32


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:30.116
Number of residues:39
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0271350.000

% Hydrophobic% Polar
41.0059.00
According to VolSite

Ligand :
3zm9_2 Structure
HET Code: QMQ
Formula: C30H34N7
Molecular weight: 492.638 g/mol
DrugBank ID: -
Buried Surface Area:61.83 %
Polar Surface area: 76.73 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 5
Aromatic rings: 5
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 10

Mass center Coordinates

XYZ
6.78551-26.7239-21.0517


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
CAICG2ILE- 1163.740Hydrophobic
CAECBARG- 1173.990Hydrophobic
CATCDARG- 1173.480Hydrophobic
CAICD1LEU- 1243.930Hydrophobic
N6OGLN- 2073.08155.08H-Bond
(Ligand Donor)
N1NILE- 2092.91173.06H-Bond
(Protein Donor)
CARCDARG- 2134.270Hydrophobic
CAHCDARG- 2133.550Hydrophobic
CAVCD2LEU- 3134.370Hydrophobic
CAHCD1ILE- 3293.670Hydrophobic
CABCE2TYR- 3334.090Hydrophobic
CAFCBTYR- 3543.70Hydrophobic
CAACD2TRP- 4203.510Hydrophobic
CABCZ3TRP- 4203.60Hydrophobic
CABCH2TRP- 4234.480Hydrophobic
CAMCH2TRP- 4233.470Hydrophobic