2C6M

Crystal structure of the human CDK2 complexed with the triazolopyrimidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2C6M/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-11-10 Released: 2005-12-07 
• Deposition Author(s): Richardson, C.M., Dokurno, P., Murray, J.B., Surgenor, A.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.270 
• R-Value Work: 0.195 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Triazolo[1,5-A]Pyrimidines as Novel Cdk2 Inhibitors: Protein Structure-Guided Design and Sar.

Richardson, C.M., Williamson, D.S., Parratt, M.J., Borgognoni, J., Cansfield, A.D., Dokurno, P., Francis, G.L., Howes, R., Moore, J.D., Murray, J.B., Robertson, A., Surgenor, A.E., Torrance, C.J.

(2006) Bioorg Med Chem Lett 16: 1353

• PubMed: 16325401 
• DOI: https://doi.org/10.1016/j.bmcl.2005.11.048
• Primary Citation of Related Structures:  
  2C68, 2C69, 2C6I, 2C6K, 2C6L, 2C6M, 2C6O, 2C6T


• PubMed Abstract: 
  

  Crystallographic and modelling data, in conjunction with a medicinal chemistry template-hopping approach, led to the identification of a series of novel and potent inhibitors of human cyclin-dependent kinase 2 (CDK2), with selectivity over glycogen synthase kinase-3beta (GSK-3beta). One example had a CDK2 IC(50) of 120 nM and showed selectivity over GSK-3beta of 167-fold.

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Organizational Affiliation: 

Vernalis (R&D) Ltd, Granta Park, Great Abington, Cambridge CB1 6GB, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34.36 kDa 
• Atom Count: 2,596 
• Modelled Residue Count: 290 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN KINASE 2	A	298	Homo sapiens	Mutation(s): 0  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941 GTEx:  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DT5	B [auth A]	4-{[5-(CYCLOHEXYLOXY)[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL]AMINO}BENZENESULFONAMIDE C17 H20 N6 O3 S RPJIMTALCNCQLV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DT5	PDBBind:  2C6M	IC50: 350 (nM) from 1 assay(s)
	BindingDB:  2C6M	IC50: 350 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.270 
• R-Value Work: 0.195 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.662	α = 90
b = 71.702	β = 90
c = 72.384	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-07 
Deposition Author(s): Richardson, C.M., Dokurno, P., Murray, J.B., Surgenor, A.E.

Revision History  

• Version 1.0: 2005-12-07
  Type: Initial release
  
• Version 1.1: 2015-09-16
  Changes: Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description