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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:

1pxk

2.800 Å

X-ray

2003-07-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cyclin-dependent kinase 2
ID:CDK2_HUMAN
AC:P24941
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.22


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:60.781
Number of residues:23
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.848469.125

% Hydrophobic% Polar
47.4852.52
According to VolSite

Ligand :
1pxk_1 Structure
HET Code: CK3
Formula: C10H12N5OS
Molecular weight: 250.300 g/mol
DrugBank ID: DB04101
Buried Surface Area:54.45 %
Polar Surface area: 113.14 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 3
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
12.229145.607223.9356


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
S4ACG2ILE- 103.780Hydrophobic
C7ACG2VAL- 183.960Hydrophobic
S4ACG1VAL- 184.370Hydrophobic
C5CBALA- 313.790Hydrophobic
C6ACD2PHE- 804.150Hydrophobic
N1NLEU- 832.82164.31H-Bond
(Protein Donor)
S4ACD2LEU- 1344.230Hydrophobic
C5CD1LEU- 1343.20Hydrophobic
C6ACBALA- 1443.530Hydrophobic