4PRJ

Aurora A kinase domain with compound 2 (N-[1-(3-cyanobenzyl)-1H-pyrazol-4-yl]-6-(1H-pyrazol-4-yl)-1H-indazole-3-carboxamide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Property- and structure-guided discovery of a tetrahydroindazole series of interleukin-2 inducible T-cell kinase inhibitors.

Burch, J.D.Lau, K.Barker, J.J.Brookfield, F.Chen, Y.Chen, Y.Eigenbrot, C.Ellebrandt, C.Ismaili, M.H.Johnson, A.Kordt, D.MacKinnon, C.H.McEwan, P.A.Ortwine, D.F.Stein, D.B.Wang, X.Winkler, D.Yuen, P.W.Zhang, Y.Zarrin, A.A.Pei, Z.

(2014) J Med Chem 57: 5714-5727

  • DOI: https://doi.org/10.1021/jm500550e
  • Primary Citation of Related Structures:  
    4PQN, 4PRJ

  • PubMed Abstract: 

    Interleukin-2 inducible T-cell kinase (ITK), a member of the Tec family of tyrosine kinases, plays a major role in T-cell signaling downstream of the T-cell receptor (TCR), and considerable efforts have been directed toward discovery of ITK-selective inhibitors as potential treatments of inflammatory disorders such as asthma. Using a previously disclosed indazole series of inhibitors as a starting point, and using X-ray crystallography and solubility forecast index (SFI) as guides, we evolved a series of tetrahydroindazole inhibitors with improved potency, selectivity, and pharmaceutical properties. Highlights include identification of a selectivity pocket above the ligand plane, and identification of appropriate lipophilic substituents to occupy this space. This effort culminated in identification of a potent and selective ITK inhibitor (GNE-9822) with good ADME properties in preclinical species.


  • Organizational Affiliation

    Genentech Inc. , 1 DNA Way, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A269Homo sapiensMutation(s): 7 
Gene Names: AURKAAIKAIRK1ARK1AURAAYK1BTAKIAK1STK15STK6
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14965 (Homo sapiens)
Explore O14965 
Go to UniProtKB:  O14965
PHAROS:  O14965
GTEx:  ENSG00000087586 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14965
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2VU
Query on 2VU

Download Ideal Coordinates CCD File 
B [auth A]N-[1-(3-cyanobenzyl)-1H-pyrazol-4-yl]-6-(1H-pyrazol-4-yl)-1H-indazole-3-carboxamide
C22 H16 N8 O
LBYBJJIMARLHMV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2VU BindingDB:  4PRJ Ki: 72 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.233 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.973α = 90
b = 81.973β = 90
c = 163.005γ = 120
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description