8G3S

MBP-Mcl1 in complex with ligand 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.145 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YLT (Subject of Investigation/LOI)
Query on YLT

Download Ideal Coordinates CCD File 
E [auth A](1'S,3aS,5R,16R,17S,19E,21S,21aR)-6'-chloro-21-methoxy-16,17-dimethyl-2,3,3',3a,4',16,17,18,21,21a-decahydro-2'H,6H,8H-15lambda~6~-spiro[10,12-etheno-15lambda~6~-furo[3,2-i][1,4]oxazepino[3,4-f][1,2,7]thiadiazacyclohexadecine-7,1'-naphthalene]-13,15,15(4H,14H)-trione
C33 H41 Cl N2 O6 S
LLLAMCJZBPYZRV-WFEBTMLYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.88α = 90
b = 137.35β = 90
c = 38.676γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
autoPROCdata reduction
autoPROCdata scaling

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 YLTClick on this verticalbar to view details

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