5VLR

CRYSTAL STRUCTURE OF PI3K DELTA IN COMPLEX WITH A TRIFLUORO-ETHYL-PYRAZOL-PYROLOTRIAZINE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of a Potent, Selective, and Efficacious Phosphatidylinositol 3-Kinase delta (PI3K delta ) Inhibitor for the Treatment of Immunological Disorders.

Liu, Q.Shi, Q.Marcoux, D.Batt, D.G.Cornelius, L.Qin, L.Y.Ruan, Z.Neels, J.Beaudoin-Bertrand, M.Srivastava, A.S.Li, L.Cherney, R.J.Gong, H.Watterson, S.H.Weigelt, C.Gillooly, K.M.McIntyre, K.W.Xie, J.H.Obermeier, M.T.Fura, A.Sleczka, B.Stefanski, K.Fancher, R.M.Padmanabhan, S.Rp, T.Kundu, I.Rajareddy, K.Smith, R.Hennan, J.K.Xing, D.Fan, J.Levesque, P.C.Ruan, Q.Pitt, S.Zhang, R.Pedicord, D.Pan, J.Yarde, M.Lu, H.Lippy, J.Goldstine, C.Skala, S.Rampulla, R.A.Mathur, A.Gupta, A.Arunachalam, P.N.Sack, J.S.Muckelbauer, J.K.Cvijic, M.E.Salter-Cid, L.M.Bhide, R.S.Poss, M.A.Hynes, J.Carter, P.H.Macor, J.E.Ruepp, S.Schieven, G.L.Tino, J.A.

(2017) J Med Chem 60: 5193-5208

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00618
  • Primary Citation of Related Structures:  
    5VLR

  • PubMed Abstract: 

    PI3Kδ plays an important role controlling immune cell function and has therefore been identified as a potential target for the treatment of immunological disorders. This article highlights our work toward the identification of a potent, selective, and efficacious PI3Kδ inhibitor. Through careful SAR, the successful replacement of a polar pyrazole group by a simple chloro or trifluoromethyl group led to improved Caco-2 permeability, reduced Caco-2 efflux, reduced hERG PC activity, and increased selectivity profile while maintaining potency in the CD69 hWB assay. The optimization of the aryl substitution then identified a 4'-CN group that improved the human/rodent correlation in microsomal metabolic stability. Our lead molecule is very potent in PK/PD assays and highly efficacious in a mouse collagen-induced arthritis model.


  • Organizational Affiliation

    Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform1,013Homo sapiensMutation(s): 0 
Gene Names: PIK3CD
EC: 2.7.1.153
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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alpha170Homo sapiensMutation(s): 4 
Gene Names: PIK3R1GRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens)
Explore P27986 
Go to UniProtKB:  P27986
PHAROS:  P27986
GTEx:  ENSG00000145675 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27986
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9EM
Query on 9EM

Download Ideal Coordinates CCD File 
C [auth A]4-acetyl-1-(3-{4-amino-5-[1-(2,2,2-trifluoroethyl)-1H-pyrazol-5-yl]pyrrolo[2,1-f][1,2,4]triazin-7-yl}phenyl)-3,3-dimethylpiperazin-2-one
C25 H25 F3 N8 O2
KSAKMNJFOKNIAA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9EM BindingDB:  5VLR IC50: min: 3, max: 71 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.847α = 90
b = 108.579β = 90
c = 142.734γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-06-07 
  • Deposition Author(s): Sack, J.S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references