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 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report



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
  • Primary Citation of Related Structures:  
    3ZC6

  • 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 within the ligand ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TYROSINE-PROTEIN KINASE JAK3ABCD288Homo sapiensMutation(s): 2 
Gene Names: JAK3
EC: 2.7.10.2 (PDB Primary Data), 2.7.1.112 (PDB Primary Data)
Find proteins for P52333 (Homo sapiens)
Explore P52333 
Go to UniProtKB:  P52333
NIH Common Fund Data Resources
PHAROS  P52333
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VFC
Query on VFC

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
PG4
Query on PG4

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

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A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A,B,C,DL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VFCIC50:  0.6000000238418579   nM  BindingDB
VFCIC50 :  0.6000000238418579   nM  PDBBind
VFCIC50:  150   nM  BindingDB
VFCIC50:  0.6000000238418579   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.17α = 90
b = 117.725β = 97.66
c = 105.831γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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