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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This is version 1.4 of the entry. See complete history


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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14351Homo sapiensMutation(s): 0 
Gene Names: MAPK14CSBPCSBP1CSBP2MXI2
EC: 2.7.1.37
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / 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
Binding Affinity Annotations 
IDSourceBinding Affinity
TZY PDBBind:  1ZZL IC50: 5 (nM) from 1 assay(s)
BindingDB:  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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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
  • Version 1.4: 2024-02-14
    Changes: Data collection