9Z4X | pdb_00009z4x

MENIN IN COMPLEX WITH JNJ-75276617 (Bleximenib)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.297 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Preclinical efficacy of the potent, selective menin-KMT2A inhibitor JNJ-75276617 (bleximenib) in KMT2A- and NPM1-altered leukemias.

Kwon, M.C.Thuring, J.W.Querolle, O.Dai, X.Verhulst, T.Pande, V.Marien, A.Goffin, D.Wenge, D.V.Yue, H.Cutler, J.A.Jin, C.Perner, F.Hogeling, S.M.Shaffer, P.L.Jacobs, F.Vinken, P.Cai, W.Keersmaekers, V.Eyassu, F.Bhogal, B.Verstraeten, K.El Ashkar, S.Perry, J.A.Jayaguru, P.Barreyro, L.Kuchnio, A.Darville, N.Krosky, D.Urbanietz, G.Verbist, B.Edwards, J.P.Cowley, G.S.Kirkpatrick, R.Steele, R.Ferrante, L.Guttke, C.Daskalakis, N.Pietsch, E.C.Wilson, D.M.Attar, R.Elsayed, Y.Fischer, E.S.Schuringa, J.J.Armstrong, S.A.Packman, K.Philippar, U.

(2024) Blood 144: 1206-1220

  • DOI: https://doi.org/10.1182/blood.2023022480
  • Primary Citation of Related Structures:  
    9Z4X

  • PubMed Abstract: 

    The interaction between menin and histone-lysine N-methyltransferase 2A (KMT2A) is a critical dependency for KMT2A- or nucleophosmin 1 (NPM1)-altered leukemias and an emerging opportunity for therapeutic development. JNJ-75276617 (bleximenib) is a novel, orally bioavailable, potent, and selective protein-protein interaction inhibitor of the binding between menin and KMT2A. In KMT2A-rearranged (KMT2A-r) and NPM1-mutant (NPM1c) acute myeloid leukemia (AML) cells, JNJ-75276617 inhibited the association of the menin-KMT2A complex with chromatin at target gene promoters, resulting in reduced expression of several menin-KMT2A target genes, including MEIS1 and FLT3. JNJ-75276617 displayed potent antiproliferative activity across several AML and acute lymphoblastic leukemia (ALL) cell lines and patient samples harboring KMT2A or NPM1 alterations in vitro. In xenograft models of AML and ALL, JNJ-75276617 reduced leukemic burden and provided a significant dose-dependent survival benefit accompanied by expression changes of menin-KMT2A target genes. JNJ-75276617 demonstrated synergistic effects with gilteritinib in vitro in AML cells harboring KMT2A-r. JNJ-75276617 further exhibited synergistic effects with venetoclax and azacitidine in AML cells bearing KMT2A-r in vitro, and significantly increased survival in mice. Interestingly, JNJ-75276617 showed potent antiproliferative activity in cell lines engineered with recently discovered mutations (MEN1M327I or MEN1T349M) that developed in patients refractory to the menin-KMT2A inhibitor revumenib. A cocrystal structure of menin in complex with JNJ-75276617 indicates a unique binding mode distinct from other menin-KMT2A inhibitors, including revumenib. JNJ-75276617 is being clinically investigated for acute leukemias harboring KMT2A or NPM1 alterations, as a monotherapy for relapsed/refractory acute leukemia (NCT04811560), or in combination with AML-directed therapies (NCT05453903).


  • Organizational Affiliation
    • Discovery Oncology, Janssen R&D, Beerse, Belgium.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Menin
A, B, C, D
539Homo sapiensMutation(s): 0 
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9N6
Query on 9N6

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
O [auth C],
Q [auth D]
N-ethyl-5-fluoro-2-{[5-(2-{(3R)-6-[(2-methoxyethyl)(methyl)amino]-2-methylhexan-3-yl}-2,6-diazaspiro[3.4]octan-6-yl)-1,2,4-triazin-6-yl]oxy}-N-(propan-2-yl)benzamide
C32 H50 F N7 O3
PDUGAXSIWNMIBQ-HHHXNRCGSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
P [auth C],
R [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.297 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.372α = 90
b = 70.486β = 91.68
c = 145.561γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release