4D0X | pdb_00004d0x

Pyrrole-3-carboxamides as potent and selective JAK2 inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4D0X/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-04-30 Released: 2014-07-23 
• Deposition Author(s): Canevari, G., Fasolini, M., Bertrand, J., Brasca, M.G., Nesi, M., Avanzi, N., Ballinari, D., Bandiera, T., Bindi, S., Carenzi, D., Casero, D., Ceriani, L., Ciomei, M., Cirla, A., Colombo, M., Cribioli, S., Cristiani, C., Della Vedova, F., Fachin, G., Felder, E.R., Galvani, A., Isacchi, A., Mirizzi, D., Motto, I., Panzeri, A., Pesenti, E., Vianello, P., Gnocchi, P., Donati, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.219 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Pyrrole-3-Carboxamides as Potent and Selective Jak2 Inhibitors.

Brasca, M.G., Nesi, M., Avanzi, N., Ballinari, D., Bandiera, T., Bertrand, J., Bindi, S., Canevari, G., Carenzi, D., Casero, D., Ceriani, L., Ciomei, M., Cirla, A., Colombo, M., Cribioli, S., Cristiani, C., Della Vedova, F., Fachin, G., Fasolini, M., Felder, E.R., Galvani, A., Isacchi, A., Mirizzi, D., Motto, I., Panzeri, A., Pesenti, E., Vianello, P., Gnocchi, P., Donati, D.

(2014) Bioorg Med Chem 22: 4998

• PubMed: 25009002 
• DOI: https://doi.org/10.1016/j.bmc.2014.06.025
• Primary Citation Related Structures: 
  4D0W, 4D0X, 4D1S


• PubMed Abstract: 
  

  We report herein the discovery, structure guided design, synthesis and biological evaluation of a novel class of JAK2 inhibitors. Optimization of the series led to the identification of the potent and orally bioavailable JAK2 inhibitor 28 (NMS-P953). Compound 28 displayed significant tumour growth inhibition in SET-2 xenograft tumour model, with a mechanism of action confirmed in vivo by typical modulation of known biomarkers, and with a favourable pharmacokinetic and safety profile.

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Organizational Affiliation: 
• Nerviano Medical Sciences S.r.l., Oncology, Viale Pasteur 10, 20014 Nerviano (MI), Italy. Electronic address: [e-mail].
Nerviano Medical Sciences S.r.l., Oncology, Viale Pasteur 10, 20014 Nerviano (MI), Italy.

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: 35.67 kDa 
• Atom Count: 2,700 
• Modeled Residue Count: 293 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN KINASE JAK2	A	298	Homo sapiens	Mutation(s): 0  EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens) Explore O60674  Go to UniProtKB:  O60674
PHAROS:  O60674 GTEx:  ENSG00000096968

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
953	B [auth A]	5-(2-aminopyrimidin-4-yl)-2-[2-chloro-5-(trifluoromethyl)phenyl]-1H-pyrrole-3-carboxamide C16 H11 Cl F3 N5 O CZUQYAXYBOEHCY-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.219 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.07	α = 90
b = 101.76	β = 90
c = 67.71	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Canevari, G., Fasolini, M., Bertrand, J., Brasca, M.G., Nesi, M., Avanzi, N., Ballinari, D., Bandiera, T., Bindi, S., Carenzi, D., Casero, D., Ceriani, L., Ciomei, M., Cirla, A., Colombo, M., Cribioli, S., Cristiani, C., Della Vedova, F., Fachin, G., Felder, E.R., Galvani, A., Isacchi, A., Mirizzi, D., Motto, I., Panzeri, A., Pesenti, E., Vianello, P., Gnocchi, P., Donati, D.

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2014-09-10
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Data collection
• Version 1.3: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation
• Version 1.4: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.6: 2024-11-06
  Changes: Structure summary