1ZZL

Crystal structure of P38 with triazolopyridine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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Literature

Theoretical and Experimental Design of Atypical Kinase Inhibitors: Application to p38 MAP Kinase.

McClure, K.F., Abramov, Y.A., Laird, E.R., Barberia, J.T., Cai, W., Carty, T.J., Cortina, S.R., Danley, D.E., Dipesa, A.J., Donahue, K.M., Dombroski, M.A., Elliott, N.C., Gabel, C.A., Han, S., Hynes, T.R., Lemotte, P.K., Mansour, M.N., Marr, E.S., Letavic, M.A., Pandit, J., Ripin, D.B., Sweeney, F.J., Tan, D., Tao, Y.

(2005) J Med Chem 48: 5728-5737

  • DOI: 10.1021/jm050346q
  • Primary Citation of Related Structures:  
    1ZZL

  • PubMed Abstract: 

    • Mimics of the benzimidazolone nucleus found in inhibitors of p38 kinase are proposed, and their theoretical potential as bioisosteres is described. A set of calculated descriptors relevant to the anticipated binding interaction for the fragments 1-methyl-1H-benzotriazole 5, 3-methyl-benzo[d]isoxazole 3, and 3-methyl-[1,2,4]triazolo[4,3-a]pyridine 4, pyridine 1, and 1,3-dimethyl-1,3-dihydro-benzoimidazol-2-one 2 are reported ...

    Mimics of the benzimidazolone nucleus found in inhibitors of p38 kinase are proposed, and their theoretical potential as bioisosteres is described. A set of calculated descriptors relevant to the anticipated binding interaction for the fragments 1-methyl-1H-benzotriazole 5, 3-methyl-benzo[d]isoxazole 3, and 3-methyl-[1,2,4]triazolo[4,3-a]pyridine 4, pyridine 1, and 1,3-dimethyl-1,3-dihydro-benzoimidazol-2-one 2 are reported. The design considerations and synthesis of p38 inhibitors based on these H-bond acceptor fragments is detailed. Comparative evaluation of the pyridine-, benzimidazolone-, benzotriazole-, and triazolopyridine-based inhibitors shows the triazoles 20 and 25 to be significantly more potent experimentally than the benzimidazolone after which they were modeled. An X-ray crystal structure of 25 bound to the active site shows that the triazole group serves as the H-bond acceptor but unexpectedly as a dual acceptor, inducing movement of the crossover connection of p38alpha. The computed descriptors for the hydrophobic and pi-pi interaction capacities were the most useful in ranking potency.

    Organizational Affiliation: 

    Pfizer Global Research and Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, USA. kim.f.mcclure@pfizer.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A351Homo sapiensMutation(s): 0 
Gene Names: MAPK14, CSBP, CSBP1, CSBP2, MXI2, CSPB1, SAPK2A
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TZY
Query on TZY
Download Ideal Coordinates CCD File 
B [auth A]6-[4-(4-FLUOROPHENYL)-1,3-OXAZOL-5-YL]-3-ISOPROPYL[1,2,4]TRIAZOLO[4,3-A]PYRIDINE
C18 H15 F N4 O
OVCXRBARSPBVMC-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TZY Binding MOAD:  1ZZL IC50: 5 (nM) from 1 assay(s)
BindingDB:  1ZZL IC50: 5 (nM) from 1 assay(s)
PDBBind:  1ZZL IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.457α = 90
b = 86.631β = 90
c = 122.857γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2005-06-14 
  • Released Date: 2005-09-13 
    • Deposition Author(s): McClure, K.F., Han, S.

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-04-13
    Changes: Database references, Derived calculations