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 5VLR | pdb_00005vlr

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 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 137.48 kDa 
  • Atom Count: 8,448 
  • Modeled Residue Count: 1,096 
  • Deposited Residue Count: 1,183 
  • 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 isoform1,013Homo 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 alpha170Homo sapiensMutation(s): 4 
Gene Names: PIK3R1, GRB1
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.279 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
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

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Ligand Structure Quality Assessment 


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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