1Y8Y | pdb_00001y8y

Crystal structure of human CDK2 complexed with a pyrazolo[1,5-a]pyrimidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1Y8Y/pdb

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


• Deposited: 2004-12-14 Released: 2005-02-08 
• Deposition Author(s): Williamson, D.S., Parratt, M.J., Torrance, C.J., Bower, J.F., Moore, J.D., Richardson, C.M., Dokurno, P., Cansfield, A.D., Francis, G.L., Hebdon, R.J., Howes, R., Jackson, P.S., Lockie, A.M., Murray, J.B., Nunns, C.L., Powles, J., Robertson, A., Surgenor, A.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.272 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Structure-guided design of pyrazolo[1,5-a]pyrimidines as inhibitors of human cyclin-dependent kinase 2.

Williamson, D.S., Parratt, M.J., Bower, J.F., Moore, J.D., Richardson, C.M., Dokurno, P., Cansfield, A.D., Francis, G.L., Hebdon, R.J., Howes, R., Jackson, P.S., Lockie, A.M., Murray, J.B., Nunns, C.L., Powles, J., Robertson, A., Surgenor, A.E., Torrance, C.J.

(2005) Bioorg Med Chem Lett 15: 863-867

• PubMed: 15686876 
• DOI: https://doi.org/10.1016/j.bmcl.2004.12.073
• Primary Citation Related Structures: 
  1Y8Y, 1Y91


• PubMed Abstract: 
  

  The protein structure guided design of a series of pyrazolo[1,5-a]pyrimidines with high potency for human cyclin-dependent kinase 2 (CDK2) is described. Some examples were shown to inhibit the growth of human colon tumour cells, were equipotent for CDK1 and were selective against GSK-3beta and other kinases.

---

Organizational Affiliation: 
• Vernalis (R&D) Ltd, Granta Park, Great Abington, Cambridge CB1 6GB, United Kingdom. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.3 kDa 
• Atom Count: 2,563 
• Modeled Residue Count: 292 
• 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  Gene Names: CDK2 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
CT7	B [auth A]	(5-CHLOROPYRAZOLO[1,5-A]PYRIMIDIN-7-YL)-(4-METHANESULFONYLPHENYL)AMINE C13 H11 Cl N4 O2 S LVNXHNRYPADEAD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CT7	BindingDB:  1Y8Y	IC50: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.272 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.944	α = 90
b = 71.756	β = 90
c = 71.957	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: 2005-02-08 
Deposition Author(s): Williamson, D.S., Parratt, M.J., Torrance, C.J., Bower, J.F., Moore, J.D., Richardson, C.M., Dokurno, P., Cansfield, A.D., Francis, G.L., Hebdon, R.J., Howes, R., Jackson, P.S., Lockie, A.M., Murray, J.B., Nunns, C.L., Powles, J., Robertson, A., Surgenor, A.E.

Revision History  

• Version 1.0: 2005-02-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description