8G3Y

MBP-Mcl1 in complex with ligand 34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of an Oral, Beyond-Rule-of-Five Mcl-1 Protein-Protein Interaction Modulator with the Potential of Treating Hematological Malignancies.

Romanov-Michailidis, F.Hsiao, C.C.Urner, L.M.Jerhaoui, S.Surkyn, M.Miller, B.Vos, A.Dominguez Blanco, M.Bueters, R.Vinken, P.Bekkers, M.Walker, D.Pietrak, B.Eyckmans, W.Dores-Sousa, J.L.Joo Koo, S.Lento, W.Bauser, M.Philippar, U.Rombouts, F.J.R.

(2023) J Med Chem 66: 6122-6148

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01953
  • Primary Citation of Related Structures:  
    8G3S, 8G3T, 8G3U, 8G3W, 8G3X, 8G3Y

  • PubMed Abstract: 

    Avoidance of apoptosis is critical for the development and sustained growth of tumors. The pro-survival protein myeloid cell leukemia 1 (Mcl-1) is an anti-apoptotic member of the Bcl-2 family of proteins which is overexpressed in many cancers. Upregulation of Mcl-1 in human cancers is associated with high tumor grade, poor survival, and resistance to chemotherapy. Therefore, pharmacological inhibition of Mcl-1 is regarded as an attractive approach to treating relapsed or refractory malignancies. Herein, we disclose the design, synthesis, optimization, and early preclinical evaluation of a potent and selective small-molecule inhibitor of Mcl-1. Our exploratory design tactics focused on structural modifications which improve the potency and physicochemical properties of the inhibitor while minimizing the risk of functional cardiotoxicity. Despite being in the "non-Lipinski" beyond-Rule-of-Five property space, the developed compound benefits from exquisite oral bioavailability in vivo and induces potent pharmacodynamic inhibition of Mcl-1 in a mouse xenograft model.


  • Organizational Affiliation

    Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltodextrin-binding protein, Induced myeloid leukemia cell differentiation protein Mcl-1 chimera518Serratia sp. FS14Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malEJW3994MCL1BCL2L3
UniProt & NIH Common Fund Data Resources
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 GroupQ07820
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-glucopyranoseB [auth R]2N/AN/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YKL (Subject of Investigation/LOI)
Query on YKL

Download Ideal Coordinates CCD File 
I [auth A]N-[(1'S,3aS,5R,15S,17S,19Z,21S,21aR)-6'-chloro-20-fluoro-21-{[(5S,9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]methyl}-21-methoxy-17-methyl-13,15-dioxo-2,3,3',3a,4,4',13,16,17,18,21,21a-dodecahydro-2'H,6H,8H-15lambda~6~-spiro[10,12-(ethanediylidene)-15lambda~6~-furo[3,2-i][1,4]oxazepino[3,4-f][1,2,7]thiadiazacyclohexadecine-7,1'-naphthalen]-15-yl]-3-methoxy-1-methyl-1H-pyrazole-4-carboxamide
C46 H59 Cl F N7 O8 S
ZIQIEGUTYXQCOR-SWIREPECSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.373α = 90
b = 136.825β = 90
c = 38.549γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection