6YBG | pdb_00006ybg

Structure of Mcl-1 in complex with compound 2g


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.235 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of S64315, a Potent and Selective Mcl-1 Inhibitor.

Szlavik, Z.Csekei, M.Paczal, A.Szabo, Z.B.Sipos, S.Radics, G.Proszenyak, A.Balint, B.Murray, J.Davidson, J.Chen, I.Dokurno, P.Surgenor, A.E.Daniels, Z.M.Hubbard, R.E.Le Toumelin-Braizat, G.Claperon, A.Lysiak-Auvity, G.Girard, A.M.Bruno, A.Chanrion, M.Colland, F.Maragno, A.L.Demarles, D.Geneste, O.Kotschy, A.

(2020) J Med Chem 63: 13762-13795

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01234
  • Primary Citation Related Structures: 
    6YBG, 6YBJ, 6YBK, 6YBL

  • PubMed Abstract: 

    Myeloid cell leukemia 1 (Mcl-1) has emerged as an attractive target for cancer therapy. It is an antiapoptotic member of the Bcl-2 family of proteins, whose upregulation in human cancers is associated with high tumor grade, poor survival, and resistance to chemotherapy. Here we report the discovery of our clinical candidate S64315, a selective small molecule inhibitor of Mcl-1. Starting from a fragment derived lead compound, we have conducted structure guided optimization that has led to a significant (3 log) improvement of target affinity as well as cellular potency. The presence of hindered rotation along a biaryl axis has conferred high selectivity to the compounds against other members of the Bcl-2 family. During optimization, we have also established predictive PD markers of Mcl-1 inhibition and achieved both efficient in vitro cell killing and tumor regression in Mcl-1 dependent cancer models. The preclinical candidate has drug-like properties that have enabled its development and entry into clinical trials.


  • Organizational Affiliation
    • Servier Research Institute of Medicinal Chemistry, Záhony u. 7, H-1031 Budapest, Hungary.

Macromolecule Content 

  • Total Structure Weight: 40.44 kDa 
  • Atom Count: 2,450 
  • Modeled Residue Count: 287 
  • Deposited Residue Count: 340 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1
A, B
170Homo sapiensMutation(s): 0 
Gene Names: MCL1BCL2L3
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

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OJT
(Subject of Investigation/LOI)

Query on OJT



Download:Ideal Coordinates CCD File
C [auth A],
E [auth B]
(2~{R})-2-[5-[3-chloranyl-2-methyl-4-[2-(4-methylpiperazin-1-yl)ethoxy]phenyl]-6-(3-chlorophenyl)thieno[2,3-d]pyrimidin-4-yl]oxy-3-(2-methoxyphenyl)propanoic acid
C36 H36 Cl2 N4 O5 S
ZDIFLDSDDULOSG-GDLZYMKVSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.235 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.749α = 90
b = 79.061β = 98.86
c = 42.294γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description