9C94 | pdb_00009c94

Crystal structure of menin in complex with inhibitor compound 20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.212 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

Design of Potent Menin-KMT2A Interaction Inhibitors with Improved In Vitro ADME Properties and Reduced hERG Affinity.

Chapsal, B.D.Kimbrough, J.R.Bester, S.M.Bergstrom, A.Backos, D.S.Campos, B.McDonald, M.G.Abrahamsen, R.Allen, A.C.Doerner Barbour, P.M.Bettendorf, T.Boys, M.L.Brown, K.Chicarelli, M.J.Cook, A.W.Crooks, A.L.Cruz, C.L.Dahlke, J.R.Eide, A.Fell, J.B.Fulton, J.L.Gargus, M.Gaudino, J.J.Guarnieri, A.L.Hansen, E.P.Holt, M.C.Kahn, D.R.Laird, E.R.Larsen, P.D.Linwood, R.Martinson, M.C.McCown, J.Mejia, M.J.Moreno, D.A.Mou, T.C.Newhouse, B.O'Leary, J.M.Rodriguez, M.E.Singh, A.Sinik, L.Strand, K.A.Touney, E.E.Wollenberg, L.A.Wong, J.Zhou, Y.Fischer, J.P.Allen, S.

(2025) ACS Med Chem Lett 16: 224-233

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00311
  • Primary Citation of Related Structures:  
    9C92, 9C93, 9C94

  • PubMed Abstract: 

    Inhibitors of the interaction of menin (MEN1) with lysine methyltransferase 2A (KMT2A) have emerged as novel therapeutic options in the treatment of genetically defined acute leukemias. Herein, we describe the structure-based design, synthesis, and biological evaluation of novel inhibitors of the menin-KMT2A interaction. Our structure-activity relationship campaign focused on achieving high antiproliferative cellular activity while mitigating risks associated with CYP3A4-dependent metabolism and hERG inhibition, which were characterized in some early clinical candidates. Our efforts resulted in the discovery of a triazine-based compound series that inhibited MV4-11 leukemia cell line proliferation with IC 50 as low as 13 nM, and selected compounds demonstrated improved in vitro ADME properties, de-risked CYP3A4 dependency, and lower hERG inhibition.


  • Organizational Affiliation

    Pfizer-Boulder, Boulder, Colorado 80301, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Menin
A, B
507Homo sapiensMutation(s): 1 
Gene Names: MEN1SCG2
UniProt & NIH Common Fund Data Resources
Find proteins for O00255 (Homo sapiens)
Explore O00255 
Go to UniProtKB:  O00255
PHAROS:  O00255
GTEx:  ENSG00000133895 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00255
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AVG (Subject of Investigation/LOI)
Query on A1AVG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
{5-fluoro-2-[(5-{7-[(1-methylcyclopropyl)methyl]-2,7-diazaspiro[3.5]nonan-2-yl}-1,2,4-triazin-6-yl)oxy]phenyl}[(1R,5S)-3-oxa-8-azabicyclo[3.2.1]octan-8-yl]methanone
C28 H35 F N6 O3
DBKDYJJSZDWBCU-OYRHEFFESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.212 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.758α = 90
b = 87.476β = 90
c = 194.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1AVGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Database references