4PRJ | pdb_00004prj

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 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2VUClick on this verticalbar to view details

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 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2VUClick on this verticalbar to view details

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