3HL7

Crystal Structure of Human p38alpha complexed with SD-0006

DOI: 10.2210/pdb3HL7/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-26 Released: 2009-07-14
Deposition Author(s): Shieh, H.-S., Kurumbail, R.G., Stegeman, R.A., Williams, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.228
R-Value Work: 0.199
R-Value Observed: 0.200

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural bioinformatics-based prediction of exceptional selectivity of p38 MAP kinase inhibitor PH-797804.

Xing, L., Shieh, H.S., Selness, S.R., Devraj, R.V., Walker, J.K., Devadas, B., Hope, H.R., Compton, R.P., Schindler, J.F., Hirsch, J.L., Benson, A.G., Kurumbail, R.G., Stegeman, R.A., Williams, J.M., Broadus, R.M., Walden, Z., Monahan, J.B.

(2009) Biochemistry 48: 6402-6411

PubMed: 19496616 Search on PubMed
DOI: 10.1021/bi900655f
Structures With Same Primary Citation

PubMed 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.

Organizational Affiliation:

Structural and Computational Chemistry, St. Louis Laboratories,Pfizer Global Research and Development, 700 Chesterfield Parkway West, Chesterfield, Missouri 63017, USA. li.xing@pfizer.com

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 0 Gene Names: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, MXI2, THP-1, SAPK2A EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens) Explore Q16539 Go to UniProtKB: Q16539
NIH Common Fund Data Resources
PHAROS Q16539 GTEx ENSG00000112062
Protein Feature View
( Mouse scroll to zoom / Hold left click to move ) Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I47 Query on I47 Download CCD File	A	2-{4-[5-(4-chlorophenyl)-4-pyrimidin-4-yl-1H-pyrazol-3-yl]piperidin-1-yl}-2-oxoethanol C₂₀ H₂₀ Cl N₅ O₂ CATQHDWESBRRQA-UHFFFAOYSA-N		Ligand Interaction
I46 Query on I46 Download CCD File	A	2-fluoro-4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine C₁₄ H₉ F₂ N₃ YJCHZVXSPFPKMX-UHFFFAOYSA-N		Ligand Interaction