3ZC6

Crystal structure of JAK3 kinase domain in complex with an indazole substituted pyrrolopyrazine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Strategic Use of Conformational Bias and Structure Based Design to Identify Potent Jak3 Inhibitors with Improved Selectivity Against the Jak Family and the Kinome.

Lynch, S.M.Devicente, J.Hermann, J.C.Jaime-Figueroa, S.Jin, S.Kuglstatter, A.Li, H.Lovey, A.Menke, J.Niu, L.Patel, V.Roy, D.Soth, M.Steiner, S.Tivitmahaisoon, P.Vu, M.D.Yee, C.

(2013) Bioorg.Med.Chem.Lett. 23: 2793

  • DOI: 10.1016/j.bmcl.2013.02.012

  • PubMed Abstract: 
  • Using a structure based design approach we have identified a series of indazole substituted pyrrolopyrazines, which are potent inhibitors of JAK3. Intramolecular electronic repulsion was used as a strategy to induce a strong conformational bias withi ...

    Using a structure based design approach we have identified a series of indazole substituted pyrrolopyrazines, which are potent inhibitors of JAK3. Intramolecular electronic repulsion was used as a strategy to induce a strong conformational bias within the ligand. Compounds bearing this conformation participated in a favorable hydrophobic interaction with a cysteine residue in the JAK3 binding pocket, which imparted high selectivity versus the kinome and improved selectivity within the JAK family.


    Organizational Affiliation

    Discovery Chemistry, Hoffmann-La Roche, pRED, Pharma Research & Early Development, 340 Kingsland Street, Nutley, NJ 07110, USA. stephen.lynch@roche.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYROSINE-PROTEIN KINASE JAK3
A, B, C, D
288Homo sapiensMutation(s): 2 
Gene Names: JAK3
EC: 2.7.10.2
Find proteins for P52333 (Homo sapiens)
Go to Gene View: JAK3
Go to UniProtKB:  P52333
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
B, C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
VFC
Query on VFC

Download SDF File 
Download CCD File 
A, B, C, D
N-[(2R)-1-(3-cyanoazetidin-1-yl)-1-oxidanylidene-propan-2-yl]-2-(6-fluoranyl-1-methyl-indazol-3-yl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide
C22 H19 F N8 O2
AGTYRXOJPORGGM-LLVKDONJSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B, C, D
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VFCIC50: 0.6 nM (99) BINDINGDB
VFCIC50: 0.6 nM BINDINGMOAD
VFCIC50: 0.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.170α = 90.00
b = 117.725β = 97.66
c = 105.831γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-25
    Type: Initial release