5S9R | pdb_00005s9r

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH BMS-986158, 2-{3-(1,4-dimethyl-1H-1,2,3-triazol-5-yl)-5-[(S)-(oxan-4-yl)(phenyl)methyl]-5H-pyrido[3,2-b]indol-7-yl}propan-2-ol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.231 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.208 (Depositor) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5S9R

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Discovery and Preclinical Pharmacology of an Oral Bromodomain and Extra-Terminal (BET) Inhibitor Using Scaffold-Hopping and Structure-Guided Drug Design.

Gavai, A.V.Norris, D.Delucca, G.Tortolani, D.Tokarski, J.S.Dodd, D.O'Malley, D.Zhao, Y.Quesnelle, C.Gill, P.Vaccaro, W.Huynh, T.Ahuja, V.Han, W.C.Mussari, C.Harikrishnan, L.Kamau, M.Poss, M.Sheriff, S.Yan, C.Marsilio, F.Menard, K.Wen, M.L.Rampulla, R.Wu, D.R.Li, J.Zhang, H.Li, P.Sun, D.Yip, H.Traeger, S.C.Zhang, Y.Mathur, A.Zhang, H.Huang, C.Yang, Z.Ranasinghe, A.Everlof, G.Raghavan, N.Tye, C.K.Wee, S.Hunt, J.T.Vite, G.Westhouse, R.Lee, F.Y.

(2021) J Med Chem 64: 14247-14265

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00625
  • Primary Citation Related Structures: 
    5S9O, 5S9P, 5S9Q, 5S9R

  • PubMed Abstract: 

    Inhibition of the bromodomain and extra-terminal (BET) family of adaptor proteins is an attractive strategy for targeting transcriptional regulation of key oncogenes, such as c-MYC. Starting with the screening hit 1 , a combination of structure-activity relationship and protein structure-guided drug design led to the discovery of a differently oriented carbazole 9 with favorable binding to the tryptophan, proline, and phenylalanine (WPF) shelf conserved in the BET family. Identification of an additional lipophilic pocket and functional group optimization to optimize pharmacokinetic (PK) properties culminated in the discovery of 18 (BMS-986158) with excellent potency in binding and functional assays. On the basis of its favorable PK profile and robust in vivo activity in a panel of hematologic and solid tumor models, BMS-986158 was selected as a candidate for clinical evaluation.


  • Organizational Affiliation
    • Research and Development, Bristol Myers Squibb Company, P. O. Box 4000, Princeton, New Jersey 08543-4000, United States.

Macromolecule Content 

  • Total Structure Weight: 16.21 kDa 
  • Atom Count: 1,121 
  • Modeled Residue Count: 126 
  • Deposited Residue Count: 128 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4128Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YWA
(Subject of Investigation/LOI)

Query on YWA



Download:Ideal Coordinates CCD File
B [auth A]2-{3-(1,4-dimethyl-1H-1,2,3-triazol-5-yl)-5-[(S)-(oxan-4-yl)(phenyl)methyl]-5H-pyrido[3,2-b]indol-7-yl}propan-2-ol
C30 H33 N5 O2
KGERZPVQIRYWRK-GDLZYMKVSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.231 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.208 (Depositor) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.6α = 90
b = 48.5β = 90
c = 58.1γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2021-09-29 
  • Deposition Author(s): Sheriff, S.

Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection
  • Version 1.3: 2026-02-18
    Changes: Refinement description, Structure summary