8SVY | pdb_00008svy

MBP-Mcl1 in complex with ligand 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 
    0.206 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Macrocyclic Carbon-Linked Pyrazoles As Novel Inhibitors of MCL-1.

Demin, S.Peschiulli, A.Velter, A.I.Vos, A.De Boeck, B.Miller, B.Rombouts, F.J.R.Reuillon, T.Lento, W.Blanco, M.D.Jouffroy, M.Steyvers, H.Bekkers, M.Altrocchi, C.Pietrak, B.Koo, S.J.Szewczuk, L.Attar, R.Philippar, U.

(2023) ACS Med Chem Lett 14: 955-961

  • DOI: https://doi.org/10.1021/acsmedchemlett.3c00141
  • Primary Citation Related Structures: 
    8SVY

  • PubMed Abstract: 

    Myeloid cell leukemia-1 (MCL-1) is a member of the antiapoptotic BCL-2 proteins family and a key regulator of mitochondrial homeostasis. Overexpression of MCL-1 is found in many cancer cells and contributes to tumor progression, which makes it an attractive therapeutic target. Pursuing our previous study of macrocyclic indoles for the inhibition of MCL-1, we report herein the impact of both pyrazole and indole isomerism on the potency and overall properties of this family of compounds. We demonstrated that the incorporation of a fluorine atom on the naphthalene moiety was a necessary step to improve cellular potency and that, combined with the introduction of various side chains on the pyrazole, it enhanced solubility significantly. This exploration culminated in the discovery of compounds ( R a )- 10 and ( R a )- 15 , possessing remarkable cellular potency and properties.


  • Organizational Affiliation
    • Janssen Research & Development, Janssen Pharmaceutica N.V., Turnhoutseweg 30, Beerse B-2340, Belgium.

Macromolecule Content 

  • Total Structure Weight: 58.74 kDa 
  • Atom Count: 5,114 
  • Modeled Residue Count: 517 
  • Deposited Residue Count: 518 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein, Induced myeloid leukemia cell differentiation protein Mcl-1 chimera518Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malEMCL1BCL2L3
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 GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseB [auth R]2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WUC
(Subject of Investigation/LOI)

Query on WUC



Download:Ideal Coordinates CCD File
H [auth A](15P)-17-chloro-33-fluoro-12-[(2-methoxyethoxy)methyl]-5,14,22-trimethyl-28-oxa-9-thia-5,6,13,14,22-pentaazaheptacyclo[27.7.1.1~4,7~.0~11,15~.0~16,21~.0~20,24~.0~30,35~]octatriaconta-1(36),4(38),6,11(15),12,16,18,20,23,29(37),30,32,34-tridecaene-23-carboxylic acid
C39 H41 Cl F N5 O5 S
QJXIDXIADATUOH-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A],
E [auth A],
F [auth A],
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.04α = 90
b = 137.032β = 90
c = 38.715γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report



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: 2023-08-09
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection