8T6F | pdb_00008t6f

Crystal structure of human MBP-Myeloid cell leukemia 1 (Mcl-1) in complex with BRD810 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YI7Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

BRD-810 is a highly selective MCL1 inhibitor with optimized in vivo clearance and robust efficacy in solid and hematological tumor models.

Rauh, U.Wei, G.Serrano-Wu, M.Kosmidis, G.Kaulfuss, S.Siegel, F.Thede, K.McFarland, J.Lemke, C.T.Werbeck, N.Nowak-Reppel, K.Pilari, S.Menz, S.Ocker, M.Zhang, W.Davis, K.Poncet-Montange, G.Roth, J.Daniels, D.Kaushik, V.K.Hubbard, B.Ziegelbauer, K.Golub, T.R.

(2024) Nat Cancer 5: 1479-1493

  • DOI: https://doi.org/10.1038/s43018-024-00814-0
  • Primary Citation of Related Structures:  
    8T6F

  • PubMed Abstract: 

    The MCL1 gene is frequently amplified in cancer and codes for the antiapoptotic protein myeloid cell leukemia 1 (MCL1), which confers resistance to the current standard of care. Therefore, MCL1 is an attractive anticancer target. Here we describe BRD-810 as a potent and selective MCL1 inhibitor and its key design principle of rapid systemic clearance to potentially minimize area under the curve-driven toxicities associated with MCL1 inhibition. BRD-810 induced rapid cell killing within 4 h in vitro but, in the same 4-h window, had no impact on cell viability or troponin I release in human induced pluripotent stem cell-derived cardiomyocytes, even at suprapharmacologic concentrations. In vivo BRD-810 induced efficacy in xenograft hematological and solid tumor models despite the short residence time of BRD-810 in plasma. In totality, our data support the hypothesis that short-term inhibition of MCL1 with BRD-810 can induce apoptosis in tumor cells while maintaining an acceptable safety profile. We, therefore, intend to advance BRD-810 to clinical trials.


  • Organizational Affiliation

    Trueline Therapeutics Inc., Cambridge, MA, USA. ulla@truelinetx.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein/Induced myeloid leukemia cell differentiation protein Mcl-1 Chimera518Escherichia coli K-12Homo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: malEb4034JW3994MCL1BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
PHAROS:  Q07820
GTEx:  ENSG00000143384 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9Q07820
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YI7 (Subject of Investigation/LOI)
Query on YI7

Download Ideal Coordinates CCD File 
D [auth A](3aM,9S,15R)-4-chloro-3-ethyl-7-{3-[(6-fluoronaphthalen-1-yl)oxy]propyl}-2-methyl-15-[2-(morpholin-4-yl)ethyl]-2,10,11,12,13,15-hexahydropyrazolo[4',3':9,10][1,6]oxazacycloundecino[8,7,6-hi]indole-8-carboxylic acid
C39 H44 Cl F N4 O5
RQXSLNDYCDRXAC-MGBGTMOVSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
F [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
YI7 BindingDB:  8T6F IC50: min: 0.37, max: 28 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.301α = 90
b = 136.957β = 90
c = 38.257γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
DIALSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YI7Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Database references, Structure summary