5CF6 | pdb_00005cf6

CRYSTAL STRUCTURE OF JANUS KINASE 2 IN COMPLEX WITH N,N-DICYCLOPROPYL-10-[(2S)-2,3-DIHYDROXYPROPYL]-3-METHYL-7-(METHYLAMINO)-3,5,8,10-TETRAAZATRICYCLO [7.3.0.02,6]DODECA-1(9),2(6),4,7,11-PENTAENE-11-CARBOXAMIDE

• PDB DOI: https://doi.org/10.2210/pdb5CF6/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-08 Released: 2015-08-26 
• Deposition Author(s): Sack, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Structure-Based Design of Selective Janus Kinase 2 Imidazo[4,5-d]pyrrolo[2,3-b]pyridine Inhibitors.

Hart, A.C., Schroeder, G.M., Wan, H., Grebinski, J., Inghrim, J., Kempson, J., Guo, J., Pitts, W.J., Tokarski, J.S., Sack, J.S., Khan, J.A., Lippy, J., Lorenzi, M.V., You, D., McDevitt, T., Vuppugalla, R., Zhang, Y., Lombardo, L.J., Trainor, G.L., Purandare, A.V.

(2015) ACS Med Chem Lett 6: 845-849

• PubMed: 26288682 
• DOI: https://doi.org/10.1021/acsmedchemlett.5b00225
• Primary Citation of Related Structures:  
  5CF4, 5CF5, 5CF6


• PubMed Abstract: 
  

  Early hit to lead work on a pyrrolopyridine chemotype provided access to compounds with biochemical and cellular potency against Janus kinase 2 (JAK2). Structure-based drug design along the extended hinge region of JAK2 led to the identification of an important H-bond interaction with the side chain of Tyr 931, which improved JAK family selectivity. The 4,5-dimethyl thiazole analogue 18 demonstrated high levels of JAK family selectivity and was identified as a promising lead for the program.

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Organizational Affiliation: 

Bristol-Myers Squibb Research & Development , Princeton, New Jersey 08543, United States.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.53 kDa 
• Atom Count: 4,992 
• Modelled Residue Count: 579 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK2	A, B	321	Homo sapiens	Mutation(s): 0  Gene Names: JAK2 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
50O	C [auth A], D [auth B]	N,N-dicyclopropyl-6-[(2S)-2,3-dihydroxypropyl]-1-methyl-4-(methylamino)-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridine-7-carboxamide C20 H26 N6 O3 FHJUPPRBBPCLDY-ZDUSSCGKSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
50O	BindingDB:  5CF6	IC50: min: 8.2, max: 720 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.64	α = 90
b = 111.64	β = 90
c = 70.417	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Sack, J.S.

Revision History  

• Version 1.0: 2015-08-26
  Type: Initial release
  
• Version 1.1: 2015-09-02
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Structure summary