8EKX

Structure of MBP-Mcl-1 in complex with MIK665


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Selective MCL-1 inhibitor ABBV-467 is efficacious in tumor models but is associated with cardiac troponin increases in patients.

Yuda, J.Will, C.Phillips, D.C.Abraham, L.Alvey, C.Avigdor, A.Buck, W.Besenhofer, L.Boghaert, E.Cheng, D.Cojocari, D.Doyle, K.Hansen, T.M.Huang, K.Johnson, E.F.Judd, A.S.Judge, R.A.Kalvass, J.C.Kunzer, A.Lam, L.T.Li, R.Martin, R.L.Mastracchio, A.Mitten, M.Petrich, A.Wang, J.Ward, J.E.Zhang, H.Wang, X.Wolff, J.E.Bell-McGuinn, K.M.Souers, A.J.

(2023) Commun Med (Lond) 3: 154-154

  • DOI: https://doi.org/10.1038/s43856-023-00380-z
  • Primary Citation of Related Structures:  
    8EKX, 8EL0, 8EL1

  • PubMed Abstract: 

    MCL-1 is a prosurvival B-cell lymphoma 2 family protein that plays a critical role in tumor maintenance and survival and can act as a resistance factor to multiple anticancer therapies. Herein, we describe the generation and characterization of the highly potent and selective MCL-1 inhibitor ABBV-467 and present findings from a first-in-human trial that included patients with relapsed/refractory multiple myeloma (NCT04178902).


  • Organizational Affiliation

    National Cancer Center Hospital East, Kashiwa, Japan.


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-1532Escherichia coli K-12Homo sapiens
This entity is chimeric
Mutation(s): 3 
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
OK5 (Subject of Investigation/LOI)
Query on OK5

Download Ideal Coordinates CCD File 
C [auth A](2~{R})-2-[5-[3-chloranyl-2-methyl-4-[2-(4-methylpiperazin-1-yl)ethoxy]phenyl]-6-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4-yl]oxy-3-[2-[[2-(2-methoxyphenyl)pyrimidin-4-yl]methoxy]phenyl]propanoic acid
C47 H44 Cl F N6 O6 S
PKYIMGFMRFVOMB-LDLOPFEMSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.362α = 90
b = 136.889β = 90
c = 38.609γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
MOLREPphasing
BUSTERrefinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release