PDBsum entry 2i40

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protein ligands Protein-protein interface(s) links
Transferase/cell cycle PDB id
Protein chains
291 a.a. *
257 a.a. *
BLZ ×2
Waters ×242
* Residue conservation analysis
PDB id:
Name: Transferase/cell cycle
Title: Cdk2/cyclin a complexed with a thiophene carboxamide inhibit
Structure: Cell division protein kinase 2. Chain: a, c. Synonym: p33 protein kinase. Engineered: yes. Cyclin-a2. Chain: b, d. Fragment: residues 173-432. Synonym: cyclin-a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: cdk2. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: ccna2, ccn1, ccna. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
2.80Å     R-factor:   0.195     R-free:   0.222
Authors: L.M.Shewchuk
Key ref: P.Bamborough et al. (2006). 5-(1H-Benzimidazol-1-yl)-3-alkoxy-2-thiophenecarbonitriles as potent, selective, inhibitors of IKK-epsilon kinase. Bioorg Med Chem Lett, 16, 6236-6240. PubMed id: 16997559 DOI: 10.1016/j.bmcl.2006.09.018
21-Aug-06     Release date:   10-Oct-06    
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Protein chains
Pfam   ArchSchema ?
P24941  (CDK2_HUMAN) -  Cyclin-dependent kinase 2
298 a.a.
291 a.a.
Protein chains
Pfam   ArchSchema ?
P20248  (CCNA2_HUMAN) -  Cyclin-A2
432 a.a.
257 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, C: E.C.  - Cyclin-dependent kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
+ protein
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cyclin-dependent protein kinase holoenzyme complex   15 terms 
  Biological process     regulation of gene silencing   30 terms 
  Biochemical function     nucleotide binding     13 terms  


DOI no: 10.1016/j.bmcl.2006.09.018 Bioorg Med Chem Lett 16:6236-6240 (2006)
PubMed id: 16997559  
5-(1H-Benzimidazol-1-yl)-3-alkoxy-2-thiophenecarbonitriles as potent, selective, inhibitors of IKK-epsilon kinase.
P.Bamborough, J.A.Christopher, G.J.Cutler, M.C.Dickson, G.W.Mellor, J.V.Morey, C.B.Patel, L.M.Shewchuk.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21329883 Y.H.Ou, M.Torres, R.Ram, E.Formstecher, C.Roland, T.Cheng, R.Brekken, R.Wurz, A.Tasker, T.Polverino, S.L.Tan, and M.A.White (2011).
TBK1 directly engages Akt/PKB survival signaling to support oncogenic transformation.
  Mol Cell, 41, 458-470.  
19834513 T.Kataoka (2009).
Chemical biology of inflammatory cytokine signaling.
  J Antibiot (Tokyo), 62, 655-667.  
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