6YTM | pdb_00006ytm

Human Brd2(BD2) L383V mutant in complex with ET-JQ1-OMe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6YTM

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Stereoselective synthesis of allele-specific BET inhibitors.

Bond, A.G.Testa, A.Ciulli, A.

(2020) Org Biomol Chem 18: 7533-7539

  • DOI: https://doi.org/10.1039/d0ob01165g
  • Primary Citation Related Structures: 
    6YTM

  • PubMed Abstract: 

    Developing stereoselective synthetic routes that are efficient and cost-effective allows easy access to biologically active molecules. Our previous syntheses of allele-selective bumped inhibitors of the Bromo and Extra-Terminal (BET) domain proteins, Brd2, Brd3, Brd4 and BrdT, required a wasteful, late-stage alkylation step and expensive chiral separation. To circumvent these limitations, we developed a route based on stereocontrolled alkylation of an N-Pf protected aspartic acid derivative that was used in a divergent, racemisation-free protocol to yield structurally diverse and enantiopure triazolodiazepines. With this approach, we synthesized bumped thienodiazepine-based BET inhibitor, ET-JQ1-OMe, in five steps and 99% ee without the need for chiral chromatography. Exquisite selectivity of ET-JQ1-OMe for Leu-Ala and Leu-Val mutants over wild-type bromodomain was established by isothermal titration calorimetry and X-ray crystallography. Our new approach provides unambiguous chemical evidence for the absolute stereochemistry of the active, allele-specific BET inhibitors and a viable route that will open wider access to this compound class.


  • Organizational Affiliation
    • Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK. a.ciulli@dundee.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 28.35 kDa 
  • Atom Count: 2,108 
  • Modeled Residue Count: 218 
  • Deposited Residue Count: 228 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 2
A, B
114Homo sapiensMutation(s): 1 
Gene Names: BRD2KIAA9001RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
PHAROS:  P25440
GTEx:  ENSG00000204256 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PMW
(Subject of Investigation/LOI)

Query on PMW



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
methyl (2R)-2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]butanoate
C22 H23 Cl N4 O2 S
WLKVOOMXHSBIOW-APWZRJJASA-N
PXN

Query on PXN



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
(2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol
C17 H36 O8
GXEZGLLPFFKHGE-FPCVCCKLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.05α = 90
b = 50.53β = 90
c = 130.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-2012-StG-311460-DrugE3CRLs

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references, Refinement description
  • Version 1.2: 2020-10-14
    Changes: Database references
  • Version 2.0: 2023-09-27
    Changes: Advisory, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Refinement description