8QSO

Crystal structure of human Mcl-1 in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.208 

Starting Model: experimental
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Literature

Development of Potent Mcl-1 Inhibitors: Structural Investigations on Macrocycles Originating from a DNA-Encoded Chemical Library Screen.

Hekking, K.F.W.Maroto, S.van Kekem, K.Haasjes, F.S.Slootweg, J.C.Oude Alink, P.G.B.Dirks, R.Sardana, M.Bolster, M.G.Kuijpers, B.Smith, D.Doodeman, R.Scheepstra, M.Zech, B.Mulvihill, M.Renzetti, L.M.Babiss, L.Centrella, P.A.Clark, M.A.Cuozzo, J.W.Guie, M.A.Sigel, E.Habeshian, S.Hupp, C.D.Liu, J.Thomson, H.A.Zhang, Y.Keefe, A.D.Muller, G.Gremmen, S.

(2024) J Med Chem 67: 3039-3065

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02206
  • Primary Citation of Related Structures:  
    8QSO

  • PubMed Abstract: 

    Evasion of apoptosis is critical for the development and growth of tumors. The pro-survival protein myeloid cell leukemia 1 (Mcl-1) is an antiapoptotic member of the Bcl-2 family, associated with tumor aggressiveness, poor survival, and drug resistance. Development of Mcl-1 inhibitors implies blocking of protein-protein interactions, generally requiring a lengthy optimization process of large, complex molecules. Herein, we describe the use of DNA-encoded chemical library synthesis and screening to directly generate complex, yet conformationally privileged macrocyclic hits that serve as Mcl-1 inhibitors. By applying a conceptual combination of conformational analysis and structure-based design in combination with a robust synthetic platform allowing rapid analoging, we optimized in vitro potency of a lead series into the low nanomolar regime. Additionally, we demonstrate fine-tuning of the physicochemical properties of the macrocyclic compounds, resulting in the identification of lead candidates 57 / 59 with a balanced profile, which are suitable for future development toward therapeutic use.


  • Organizational Affiliation

    Symeres, 6546BB Nijmegen, The Netherlands.


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-1518Homo sapiensMutation(s): 0 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WXW (Subject of Investigation/LOI)
Query on WXW

Download Ideal Coordinates CCD File 
C [auth A] (13S,16R,19S)-16-benzyl-43-ethoxy-N-methyl-7,11,14,17-tetraoxo-13-phenyl-5-oxa-2,8,12,15,18-pentaaza-1(1,4),4(1,2)-dibenzena-9(1,4)-cyclohexanacycloicosaphane-19-carboxamide
C46 H54 N6 O7
SRUXQNNPEVMXJL-OPWBMBNNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.528α = 90
b = 90.804β = 90
c = 94.104γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references