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


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
  • Structures With Same Primary Citation

  • 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 poc ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoformA1015Homo sapiensMutation(s): 0 
Gene Names: PIK3CD
EC: 2.7.1.153
Find proteins for O00329 (Homo sapiens)
Explore O00329 
Go to UniProtKB:  O00329
NIH Common Fund Data Resources
PHAROS  O00329
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alphaB169Bos taurusMutation(s): 0 
Gene Names: PIK3R1
Find proteins for P23727 (Bos taurus)
Explore P23727 
Go to UniProtKB:  P23727
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 CCD File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
799Ki:  0.09000000357627869   nM  BindingDB
799Ki:  0.07999999821186066   nM  BindingDB
799Ki:  23.700000762939453   nM  BindingDB
799Ki:  0.11999999731779099   nM  BindingDB
799Ki:  23.700000762939453   nM  BindingDB
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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