5VLR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.7b00618

  • 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, an ...

    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

    Department of Discovery Synthesis, Biocon Bristol-Myers Squibb Research Centre , Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bengaluru 560099, India.,Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
A
1013Homo sapiensMutation(s): 0 
Gene Names: PIK3CD
EC: 2.7.1.153
Find proteins for O00329 (Homo sapiens)
Go to Gene View: PIK3CD
Go to UniProtKB:  O00329
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alpha
B
170Homo sapiensMutation(s): 4 
Gene Names: PIK3R1 (GRB1)
Find proteins for P27986 (Homo sapiens)
Go to Gene View: PIK3R1
Go to UniProtKB:  P27986
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9EM
Query on 9EM

Download SDF File 
Download CCD File 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 90.847α = 90.00
b = 108.579β = 90.00
c = 142.734γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-04-26 
  • Released Date: 2017-06-07 
  • Deposition Author(s): Sack, J.S.

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references