1ZYJ

Human P38 MAP Kinase in Complex with Inhibitor 1a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Two classes of p38alpha MAP kinase inhibitors having a common diphenylether core but exhibiting divergent binding modes.

Michelotti, E.L.Moffett, K.K.Nguyen, D.Kelly, M.J.Shetty, R.Chai, X.Northrop, K.Namboodiri, V.Campbell, B.Flynn, G.A.Fujimoto, T.Hollinger, F.P.Bukhtiyarova, M.Springman, E.B.Karpusas, M.

(2005) Bioorg Med Chem Lett 15: 5274-5279

  • DOI: https://doi.org/10.1016/j.bmcl.2005.08.038
  • Primary Citation of Related Structures:  
    1ZYJ, 1ZZ2

  • PubMed Abstract: 

    Two new classes of diphenylether inhibitors of p38alpha MAP kinase are described. Both chemical classes are based on a common diphenylether core that is identified by simulated fragment annealing as one of the most favored chemotypes within a prominent hydrophobic pocket of the p38alpha ATP-binding site. In the fully elaborated molecules, the diphenylether moiety acts as an anchor occupying the deep pocket, while polar extensions make specific interactions with either the adenine binding site or the phosphate binding site of ATP. The synthesis, crystallographic analysis, and biological activity of these p38alpha inhibitors are discussed.


  • Organizational Affiliation

    Department of Chemistry, Locus Pharmaceuticals, Inc., Four Valley Square, 512 Township Line Rd, Blue Bell, PA 19422, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BI5
Query on BI5

Download Ideal Coordinates CCD File 
C [auth A]4-PHENOXY-N-(PYRIDIN-2-YLMETHYL)BENZAMIDE
C19 H16 N2 O2
HVLSCZSVTCNAQX-UHFFFAOYSA-N
BOG
Query on BOG

Download Ideal Coordinates CCD File 
B [auth A]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BI5 PDBBind:  1ZYJ IC50: 1500 (nM) from 1 assay(s)
BindingDB:  1ZYJ IC50: 1500 (nM) from 1 assay(s)
Binding MOAD:  1ZYJ IC50: 1500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.76α = 90
b = 70.92β = 90
c = 75.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-08
    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: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary