5T8F | pdb_00005t8f

p110delta/p85alpha with taselisib (GDC-0032)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 
    0.304 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.6b01363
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 137.53 kDa 
  • Atom Count: 8,537 
  • Modeled Residue Count: 1,090 
  • Deposited Residue Count: 1,184 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform1,015Homo 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
GTEx:  ENSG00000171608 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00329
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alpha169Bos 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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free:  0.304 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
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
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description