5MZ3

P38 ALPHA MUTANT C162S IN COMPLEX WITH CMPD2 [N-(4-Methyl-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl)-3-(trifluoromethyl)benzamide]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Imidazo[1,2-a]pyridin-6-yl-benzamide analogs as potent RAF inhibitors.

Smith, A.Ni, Z.J.Poon, D.Huang, Z.Chen, Z.Zhang, Q.Tandeske, L.Merritt, H.Shoemaker, K.Chan, J.Kaufman, S.Huh, K.Murray, J.Appleton, B.A.Cowan-Jacob, S.W.Scheufler, C.Kanazawa, T.Jansen, J.M.Stuart, D.Shafer, C.M.

(2017) Bioorg Med Chem Lett 27: 5221-5224

  • DOI: 10.1016/j.bmcl.2017.10.047
  • Primary Citation of Related Structures:  
    5MZ3, 6B8U

  • PubMed Abstract: 
  • A series of imidazo[1,2-a]pyridin-6-yl-benzamide analogs was designed as inhibitors of B-RAF V600E . Medicinal chemistry techniques were employed to explore the SAR for this series and improve selectivity versus P38 and VEGFR2.


    Organizational Affiliation

    Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, CA 94608, United States. Electronic address: cynthia.shafer@novartis.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A369Homo sapiensMutation(s): 1 
Gene Names: MAPK14CSBPCSBP1CSBP2CSPB1MXI2SAPK2A
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
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
8EN
Query on 8EN

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[3-(2-acetamidoimidazo[1,2-a]pyridin-6-yl)-4-methyl-phenyl]-3-(trifluoromethyl)benzamide
C24 H19 F3 N4 O2
MRTHXFZEQBERDI-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
8EN Binding MOAD:  5MZ3 IC50: 0.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.919α = 90
b = 85.607β = 90
c = 127.468γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references
  • Version 1.2: 2018-11-07
    Changes: Data collection, Source and taxonomy, Structure summary