2I40

Cdk2/Cyclin A complexed with a thiophene carboxamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2I40/pdb

• Classification: transferase/cell cycle
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-08-21 Released: 2006-10-10 
• Deposition Author(s): Shewchuk, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.222 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

5-(1H-Benzimidazol-1-yl)-3-alkoxy-2-thiophenecarbonitriles as potent, selective, inhibitors of IKK-epsilon kinase

Bamborough, P., Christopher, J.A., Cutler, G.J., Dickson, M.C., Mellor, G.W., Morey, J.V., Patel, C.B., Shewchuk, L.M.

(2006) Bioorg Med Chem Lett 16: 6236-6240

• PubMed: 16997559 
• DOI: https://doi.org/10.1016/j.bmcl.2006.09.018
• Primary Citation of Related Structures:  
  2I40


• PubMed Abstract: 
  

  The identification and hit-to-lead exploration of a novel, potent and selective series of substituted benzimidazole-thiophene carbonitrile inhibitors of IKK-epsilon kinase is described. Compound 12e was identified with an IKK-epsilon enzyme potency of pIC(50) 7.4, and has a highly encouraging wider selectivity profile, including selectivity within the IKK kinase family.

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Organizational Affiliation: 

GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 128.6 kDa 
• Atom Count: 9,109 
• Modelled Residue Count: 1,099 
• Deposited Residue Count: 1,116 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A, C	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2 EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens) Explore P24941  Go to UniProtKB:  P24941
PHAROS:  P24941 GTEx:  ENSG00000123374

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-A2	B, D	260	Homo sapiens	Mutation(s): 0  Gene Names: CCNA2, CCN1, CCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens) Explore P20248  Go to UniProtKB:  P20248
PHAROS:  P20248 GTEx:  ENSG00000145386

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLZ	E [auth A], F [auth C]	5-[5,6-BIS(METHYLOXY)-1H-BENZIMIDAZOL-1-YL]-3-{[1-(2-CHLOROPHENYL)ETHYL]OXY}-2-THIOPHENECARBOXAMIDE C22 H20 Cl N3 O4 S UHCHLTQBLNUYRT-GFCCVEGCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BLZ	PDBBind:  2I40	IC50: 1580 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.222 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.882	α = 90
b = 184.882	β = 90
c = 213	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-10 
Deposition Author(s): Shewchuk, L.M.

Revision History  

• Version 1.0: 2006-10-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description