8G3Y | pdb_00008g3y

MBP-Mcl1 in complex with ligand 34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.216 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8G3Y

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 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.

Macromolecule Content 

  • Total Structure Weight: 58.94 kDa 
  • Atom Count: 4,639 
  • Modeled Residue Count: 515 
  • Deposited Residue Count: 518 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 GlycosylationD 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 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
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