5T8F

p110delta/p85alpha with taselisib (GDC-0032)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Design of Tricyclic NF-kappa B Inducing Kinase (NIK) Inhibitors That Have High Selectivity over Phosphoinositide-3-kinase (PI3K).

Castanedo, G.M.Blaquiere, N.Beresini, M.Bravo, B.Brightbill, H.Chen, J.Cui, H.F.Eigenbrot, C.Everett, C.Feng, J.Godemann, R.Gogol, E.Hymowitz, S.Johnson, A.Kayagaki, N.Kohli, P.B.Knuppel, K.Kraemer, J.Kruger, S.Loke, P.McEwan, P.Montalbetti, C.Roberts, D.A.Smith, M.Steinbacher, S.Sujatha-Bhaskar, S.Takahashi, R.Wang, X.Wu, L.C.Zhang, Y.Staben, S.T.

(2017) J Med Chem 60: 627-640

  • DOI: 10.1021/acs.jmedchem.6b01363
  • Primary Citation of Related Structures:  
    5T8F, 5T8O, 5T8P, 5T8Q

  • PubMed Abstract: 
  • We report here structure-guided optimization of a novel series of NF-κB inducing kinase (NIK) inhibitors. Starting from a modestly potent, low molecular weight lead, activity was improved by designing a type 11/2 binding mode that accessed a back pocket past the methionine-471 gatekeeper ...

    We report here structure-guided optimization of a novel series of NF-κB inducing kinase (NIK) inhibitors. Starting from a modestly potent, low molecular weight lead, activity was improved by designing a type 11/2 binding mode that accessed a back pocket past the methionine-471 gatekeeper. Divergent binding modes in NIK and PI3K were exploited to dampen PI3K inhibition while maintaining NIK inhibition within these series. Potent compounds were discovered that selectively inhibit the nuclear translocation of NF-κB2 (p52/REL-B) but not canonical NF-κB1 (REL-A/p50).


    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
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoformA1015Homo sapiensMutation(s): 0 
Gene Names: PIK3CD
EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O00329 (Homo sapiens)
Explore O00329 
Go to UniProtKB:  O00329
PHAROS:  O00329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00329
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alphaB169Bos taurusMutation(s): 0 
Gene Names: PIK3R1
UniProt
Find proteins for P23727 (Bos taurus)
Explore P23727 
Go to UniProtKB:  P23727
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23727
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
799
Query on 799

Download Ideal Coordinates CCD File 
C [auth A]2-methyl-2-(4-{2-[3-methyl-1-(propan-2-yl)-1H-1,2,4-triazol-5-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepin-9-yl}-1H-pyrazol-1-yl)propanamide
C24 H28 N8 O2
BEUQXVWXFDOSAQ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
799 BindingDB:  5T8F Ki: min: 0.08, max: 23.7 (nM) from 6 assay(s)
IC50: 0.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.096α = 90
b = 108.604β = 90
c = 142.223γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-02-08
    Changes: Database references