5AEP | pdb_00005aep

Novel pyrrole carboxamide inhibitors of JAK2 as potential treatment of myeloproliferative disorders

• PDB DOI: https://doi.org/10.2210/pdb5AEP/pdb

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


• Deposited: 2015-01-08 Released: 2015-04-29 
• Deposition Author(s): Canevari, G., Bertrand, J., Brasca, M.G., Nesi, M., Amboldi, N., Avanzi, N., Bindi, S., Casero, D., Ciomei, M., Colombo, N., Cribioli, S., Fachin, G., Felder, E.R., Galvani, A., Isacchi, A., Motto, I., Panzeri, A., Gnocchi, P., Donati, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Novel Pyrrole Carboxamide Inhibitors of Jak2 as Potential Treatment of Myeloproliferative Disorders.

Brasca, M.G., Gnocchi, P., Nesi, M., Amboldi, N., Avanzi, N., Bertrand, J., Bindi, S., Canevari, G., Casero, D., Ciomei, M., Colombo, N., Cribioli, S., Fachin, G., Felder, E.R., Galvani, A., Isacchi, A., Motto, I., Panzeri, A., Donati, D.

(2015) Bioorg Med Chem 23: 2387

• PubMed: 25882525 
• DOI: https://doi.org/10.1016/j.bmc.2015.03.059
• Primary Citation Related Structures: 
  5AEP


• PubMed Abstract: 
  

  Compound 1, a hit from the screening of our chemical collection displaying activity against JAK2, was deconstructed for SAR analysis into three regions, which were explored. A series of compounds was synthesized leading to the identification of the potent and orally bioavailable JAK2 inhibitor 16 (NMS-P830), which showed an encouraging tumour growth inhibition in SET-2 xenograft tumour model, with evidence for JAK2 pathway suppression demonstrated by in vivo pharmacodynamic effects.

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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: 35.55 kDa 
• Atom Count: 2,588 
• Modeled Residue Count: 289 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QUP	B [auth A]	1-(5-chloro-2-methylphenyl)-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yl)-1H-pyrrole-2-carboxamide C18 H14 Cl N5 O LCPNDRXSKAUPSE-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: 1.95 Å
• R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.74	α = 90
b = 101.26	β = 90
c = 67.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-29 
Deposition Author(s): Canevari, G., Bertrand, J., Brasca, M.G., Nesi, M., Amboldi, N., Avanzi, N., Bindi, S., Casero, D., Ciomei, M., Colombo, N., Cribioli, S., Fachin, G., Felder, E.R., Galvani, A., Isacchi, A., Motto, I., Panzeri, A., Gnocchi, P., Donati, D.

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 1.1: 2015-05-13
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Data collection
• Version 1.3: 2019-04-24
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.5: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2024-11-20
  Changes: Structure summary