9PQ6 | pdb_00009pq6

MBP-Mcl1 in complex with ligand 12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.211 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9PQ6

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

In Pursuit of Best-in-Class MCL-1 Inhibitors: Discovery of Highly Potent 1,4-Indoyl Macrocycles with Favorable Physicochemical Properties.

Velter, I.A.Lento, W.Peschiulli, A.Reuillon, T.D.Ferrer, S.Orgaz-Gordillo, S.Buijnsters, P.De Boeck, B.C.A.G.Demin, S.Van Roosbroeck, Y.Jouffroy, M.Vos, A.Miller, B.Shaffer, P.Koo, S.J.Dominguez Blanco, M.McQueen, L.Altrocchi, C.Bueters, R.Vinken, P.Bekkers, M.Steyvers, H.Guttke, C.Walker, D.Bauser, M.Wilson, D.M.Philippar, U.Rombouts, F.J.R.

(2025) J Med Chem 68: 16989-17029

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c03166
  • Primary Citation Related Structures: 
    9PQ5, 9PQ6, 9PQ7

  • PubMed Abstract: 

    Myeloid Cell Leukemia 1, or MCL-1, is an anti-apoptotic protein belonging to the BCL-2 family of proteins, which regulate the mitochondrial pathway of cellular apoptosis via binding of pro- and anti-apoptotic family members. Genetic amplification and overexpression of MCL-1 is one mechanism cancer cells utilize to avoid death and thus MCL-1 has emerged as an attractive target for cancer treatment. Herein, we describe our strategy and medicinal chemistry efforts to identify best-in-class MCL-1 inhibitors with high cytotoxic potency and improved biorelevant solubility while aiming to maximize therapeutic index versus on-target toxicity via IV dosing. These efforts led to the discovery of JNJ-78394355: a highly efficient anti-tumor agent, as demonstrated by the in vivo studies in human-xenograft mouse models of acute myeloid leukemia (AML) and multiple myeloma (MM).


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

Macromolecule Content 

  • Total Structure Weight: 58.62 kDa 
  • Atom Count: 4,898 
  • 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
Maltose/maltodextrin-binding periplasmic protein,Induced myeloid leukemia cell differentiation protein Mcl-1518Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994MCL1BCL2L3
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-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CMH
(Subject of Investigation/LOI)

Query on A1CMH



Download:Ideal Coordinates CCD File
C [auth A]17-chloranyl-33-fluoranyl-5,13,14,22-tetramethyl-28-oxa-9-thia-5,6,12,13,24-pentazaheptacyclo[27.7.1.1^{4,7}.0^{11,15}.0^{16,21}.0^{20,24}.0^{30,35}]octatriaconta-1(36),4(38),6,11,14,16,18,20,22,29(37),30(35),31,33-tridecaene-23-carboxylic acid
C36 H35 Cl F N5 O3 S
UFDPXRGNCBNUQX-UHFFFAOYSA-N
EDO

Query on EDO



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

Query on FMT



Download:Ideal Coordinates CCD File
H [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free:  0.211 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.573α = 90
b = 137.15β = 90
c = 38.524γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
REFMACrefinement
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

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: 2025-10-08
    Type: Initial release