1R78

CDK2 complex with a 4-alkynyl oxindole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1R78/pdb

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


• Deposited: 2003-10-20 Released: 2004-01-20 
• Deposition Author(s): Luk, K.-C., Simcox, M.E., Schutt, A., Rowan, K., Thompson, T., Chen, Y., Kammlott, U., DePinto, W., Dunten, P., Dermatakis, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.262 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Literature

A new series of potent oxindole inhibitors of CDK2

Luk, K.-C., Simcox, M.E., Schutt, A., Rowan, K., Thompson, T., Chen, Y., Kammlott, U., DePinto, W., Dunten, P., Dermatakis, A.

(2004) Bioorg Med Chem Lett 14: 913-917

• PubMed: 15012993 
• DOI: https://doi.org/10.1016/j.bmcl.2003.12.009
• Primary Citation of Related Structures:  
  1R78


• PubMed Abstract: 
  

  A novel series of oxindole-type inhibitors of CDK2 that have heteroatom substituted alkynyl moieties at their C-4 position is described. These novel 4-alkynyl-substituted inhibitors have superior potency relative to their parent compound in free enzyme and in cell based assays. The crystal structure of CDK2 in complex with one of these analogues was determined and gives insight to their increased potency. The biochemical evaluation of a representative derivative is also described.

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Organizational Affiliation: 

Hoffmann-La Roche Inc., 340 Kingsland St., Nutley, NJ 07110-1199, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.36 kDa 
• Atom Count: 2,309 
• Modelled Residue Count: 273 
• 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 (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
FMD	B [auth A]	4-((3R,4S,5R)-4-AMINO-3,5-DIHYDROXY-HEX-1-YNYL)-5-FLUORO-3-[1-(3-METHOXY-1H-PYRROL-2-YL)-METH-(Z)-YLIDENE]-1,3-DIHYDRO-INDOL-2-ONE C20 H20 F N3 O4 RAKYKJWUUUKCCW-MPLBGYFPSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FMD	PDBBind:  1R78	IC50: 3 (nM) from 1 assay(s)
	BindingDB:  1R78	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.262 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.88	α = 90
b = 71.962	β = 90
c = 72.779	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-20 
Deposition Author(s): Luk, K.-C., Simcox, M.E., Schutt, A., Rowan, K., Thompson, T., Chen, Y., Kammlott, U., DePinto, W., Dunten, P., Dermatakis, A.

Revision History  

• Version 1.0: 2004-01-20
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations