5MZ3 | pdb_00005mz3

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]

• PDB DOI: https://doi.org/10.2210/pdb5MZ3/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2017-01-30 Released: 2017-11-15 
• Deposition Author(s): Cowan-Jacob, S.W., Scheufler, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.197 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

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

• PubMed: 29107542 
• DOI: https://doi.org/10.1016/j.bmcl.2017.10.047
• Primary Citation 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.

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Organizational Affiliation: 
• Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, CA 94608, United States.
Novartis Institutes of Biomedical Research, Novartis Campus, CH-4056 Basel, Switzerland.
Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, CA 94608, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.9 kDa 
• Atom Count: 3,123 
• Modeled Residue Count: 350 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	369	Homo sapiens	Mutation(s): 1  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A 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 GTEx:  ENSG00000112062

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8EN	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.197 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.919	α = 90
b = 85.607	β = 90
c = 127.468	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
BUSTER	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Cowan-Jacob, S.W., Scheufler, C.

Revision History  

• 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
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references