3RVG | pdb_00003rvg

Crystals structure of Jak2 with a 1-amino-5H-pyrido[4,3-b]indol-4-carboxamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.300 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of 1-amino-5H-pyrido[4,3-b]indol-4-carboxamide inhibitors of Janus kinase 2 (JAK2) for the treatment of myeloproliferative disorders.

Lim, J.Taoka, B.Otte, R.D.Spencer, K.Dinsmore, C.J.Altman, M.D.Chan, G.Rosenstein, C.Sharma, S.Su, H.P.Szewczak, A.A.Xu, L.Yin, H.Zugay-Murphy, J.Marshall, C.G.Young, J.R.

(2011) J Med Chem 54: 7334-7349

  • DOI: https://doi.org/10.1021/jm200909u
  • Primary Citation Related Structures: 
    3RVG

  • PubMed Abstract: 

    The JAK-STAT pathway mediates signaling by cytokines, which control survival, proliferation, and differentiation of a variety of cells. In recent years, a single point mutation (V617F) in the tyrosine kinase JAK2 was found to be present with a high incidence in myeloproliferative disorders (MPDs). This mutation led to hyperactivation of JAK2, cytokine-independent signaling, and subsequent activation of downstream signaling networks. The genetic, biological, and physiological evidence suggests that JAK2 inhibitors could be effective in treating MPDs. De novo design efforts of new scaffolds identified 1-amino-5H-pyrido[4,3-b]indol-4-carboxamides as a new viable lead series. Subsequent optimization of cell potency, metabolic stability, and off-target activities of the leads led to the discovery of 7-(2-aminopyrimidin-5-yl)-1-{[(1R)-1-cyclopropyl-2,2,2-trifluoroethyl]amino}-5H-pyrido[4,3-b]indole-4-carboxamide (65). Compound 65 is a potent, orally active inhibitor of JAK2 with excellent selectivity, PK profile, and in vivo efficacy in animal models.


  • Organizational Affiliation
    • Department of Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States. jongwon_lim@merck.com

Macromolecule Content 

  • Total Structure Weight: 36.18 kDa 
  • Atom Count: 2,399 
  • Modeled Residue Count: 287 
  • Deposited Residue Count: 303 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK2303Homo sapiensMutation(s): 0 
Gene Names: JAK2
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens)
Explore O60674 
Go to UniProtKB:  O60674
PHAROS:  O60674
GTEx:  ENSG00000096968 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60674
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
17P

Query on 17P



Download:Ideal Coordinates CCD File
B [auth A]1-(cyclohexylamino)-7-(1-methyl-1H-pyrazol-4-yl)-5H-pyrido[4,3-b]indole-4-carboxamide
C22 H24 N6 O
NSYNFVRSQTTZAL-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.300 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.433α = 90
b = 124.433β = 90
c = 36.734γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary