2V0D

Crystal structure of human CDK2 complexed with a thiazolidinone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2V0D/pdb

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


• Deposited: 2007-05-14 Released: 2007-06-26 
• 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: 2.20 Å
• R-Value Free: 0.286 
• R-Value Work: 0.193 
• R-Value Observed: 0.197 

Literature

Discovery of a Potent Cdk2 Inhibitor with a Novel Binding Mode, Using Virtual Screening and Initial, Structure-Guided Lead Scoping.

Richardson, C.M., Nunns, C.L., Williamson, D.S., Parratt, M.J., Dokurno, P., Howes, R., Borgognoni, J., Drysdale, M.J., Finch, H., Hubbard, R.E., Jackson, P.S., Kierstan, P., Lentzen, G., Moore, J.D., Murray, J.B., Simmonite, H., Surgenor, A.E., Torrance, C.J.

(2007) Bioorg Med Chem Lett 17: 3880

• PubMed: 17570665 
• DOI: https://doi.org/10.1016/j.bmcl.2007.04.110
• Primary Citation of Related Structures:  
  2UZB, 2UZD, 2UZE, 2UZL, 2UZN, 2UZO, 2V0D


• PubMed Abstract: 
  

  Virtual screening against a pCDK2/cyclin A crystal structure led to the identification of a potent and novel CDK2 inhibitor, which exhibited an unusual mode of interaction with the kinase binding motif. With the aid of X-ray crystallography and modelling, a medicinal chemistry strategy was implemented to probe the interactions seen in the crystal structure and to establish SAR. A fragment-based approach was also considered but a different, more conventional, binding mode was observed. Compound selectivity against GSK-3beta was improved using a rational design strategy, with crystallographic verification of the CDK2 binding mode.

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Organizational Affiliation: 

Vernalis (R&D) Ltd, Granta Park, Cambridge CB21 6GB, UK. [e-mail]

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: 34.22 kDa 
• Atom Count: 2,579 
• Modelled 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  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (PDB Primary Data)
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C53	B [auth A]	2-IMINO-5-(1-PYRIDIN-2-YL-METH-(E)-YLIDENE)-1,3-THIAZOLIDIN-4-ONE C9 H7 N3 O S LHGOQMPIWSCKBA-FNORWQNLSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.286 
• R-Value Work: 0.193 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.459	α = 90
b = 71.85	β = 90
c = 72.011	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Richardson, C.M., Dokurno, P., Murray, J.B., Surgenor, A.E.

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references