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PDBsum entry 3hll

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protein ligands links
Transferase PDB id
3hll
Jmol
Contents
Protein chain
337 a.a. *
Ligands
I45
I46
PO2
Waters ×203
* Residue conservation analysis
PDB id:
3hll
Name: Transferase
Title: Crystal structure of human p38alpha complexed with ph-797804
Structure: Mitogen-activated protein kinase 14. Chain: a. Synonym: mitogen-activated protein kinase p38 alpha, map ki alpha, cytokine suppressive anti-inflammatory drug-binding csaid-binding protein, csbp, max-interacting protein 2, map mxi2, sapk2a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: csbp, csbp1, csbp2, cspb1, mapk14, mxi2, thp-1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.95Å     R-factor:   0.219     R-free:   0.254
Authors: H.-S.Shieh,J.M.Williams,R.A.Stegeman,R.G.Kurumbail
Key ref: L.Xing et al. (2009). Structural bioinformatics-based prediction of exceptional selectivity of p38 MAP kinase inhibitor PH-797804. Biochemistry, 48, 6402-6411. PubMed id: 19496616 DOI: 10.1021/bi900655f
Date:
27-May-09     Release date:   14-Jul-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q16539  (MK14_HUMAN) -  Mitogen-activated protein kinase 14
Seq:
Struc:
360 a.a.
337 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.11.24  - Mitogen-activated protein kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
= ADP
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell   8 terms 
  Biological process     intracellular signal transduction   71 terms 
  Biochemical function     nucleotide binding     11 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi900655f Biochemistry 48:6402-6411 (2009)
PubMed id: 19496616  
 
 
Structural bioinformatics-based prediction of exceptional selectivity of p38 MAP kinase inhibitor PH-797804.
L.Xing, H.S.Shieh, S.R.Selness, R.V.Devraj, J.K.Walker, B.Devadas, H.R.Hope, R.P.Compton, J.F.Schindler, J.L.Hirsch, A.G.Benson, R.G.Kurumbail, R.A.Stegeman, J.M.Williams, R.M.Broadus, Z.Walden, J.B.Monahan.
 
  ABSTRACT  
 
PH-797804 is a diarylpyridinone inhibitor of p38alpha mitogen-activated protein (MAP) kinase derived from a racemic mixture as the more potent atropisomer (aS), first proposed by molecular modeling and subsequently confirmed by experiments. On the basis of structural comparison with a different biaryl pyrazole template and supported by dozens of high-resolution crystal structures of p38alpha inhibitor complexes, PH-797804 is predicted to possess a high level of specificity across the broad human kinase genome. We used a structural bioinformatics approach to identify two selectivity elements encoded by the TXXXG sequence motif on the p38alpha kinase hinge: (i) Thr106 that serves as the gatekeeper to the buried hydrophobic pocket occupied by 2,4-difluorophenyl of PH-797804 and (ii) the bidentate hydrogen bonds formed by the pyridinone moiety with the kinase hinge requiring an induced 180 degrees rotation of the Met109-Gly110 peptide bond. The peptide flip occurs in p38alpha kinase due to the critical glycine residue marked by its conformational flexibility. Kinome-wide sequence mining revealed rare presentation of the selectivity motif. Corroboratively, PH-797804 exhibited exceptionally high specificity against MAP kinases and the related kinases. No cross-reactivity was observed in large panels of kinase screens (selectivity ratio of >500-fold). In cellular assays, PH-797804 demonstrated superior potency and selectivity consistent with the biochemical measurements. PH-797804 has met safety criteria in human phase I studies and is under clinical development for several inflammatory conditions. Understanding the rationale for selectivity at the molecular level helps elucidate the biological function and design of specific p38alpha kinase inhibitors.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20626350 A.Cuadrado, and A.R.Nebreda (2010).
Mechanisms and functions of p38 MAPK signalling.
  Biochem J, 429, 403-417.  
19942586 D.Huang, T.Zhou, K.Lafleur, C.Nevado, and A.Caflisch (2010).
Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis.
  Bioinformatics, 26, 198-204.  
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