Oncofusion

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Interfaceestablished confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.Q5-interfaces

The menin–KMT2A grip (MBM1), the interface the drugs actually block

also called MBM1 · menin-binding motif 1 · RWRFP motif · menin-MLL interface

The first dozen amino acids of KMT2A plug into a pocket on menin like a key in a lock. Every approved and experimental menin drug works by filling that pocket so the key cannot go in.

The same thing, for a scientist

KMT2A residues 4-15, with the core RWRFP motif at 6-10, insert into the central cavity of menin's TPR core. This motif is retained in every KMT2A fusion protein, which is why the interface is a fusion-agnostic target. A second, much weaker motif (MBM2, residues 23-40) binds the same protein with roughly 20-fold lower affinity.

loading 4GQ6…
PDB 4GQ6menin + KMT2A MBM1
Menin, with the first few amino acids of KMT2A threaded into its central pocket.
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The peptide shown is KMT2A residues 6-15, resolved at 1.55 Å.

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Phe9 of KMT2A buries into the deepest part of the cavity; replacing it with alanine costs about 160-fold in binding.

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Every approved menin inhibitor occupies approximately this volume, which is why a fusion with any partner is still sensitive.

Go deeper
The numbers that matter1 deeper

Affinities measured by isothermal titration calorimetry and fluorescence polarisation 1:

PeptideAffinity (Kd)Method
KMT2A 4-15 (MBM1)53 nMfluorescence polarisation
KMT2A 4-15 (MBM1)72 nMcalorimetry
KMT2A 23-40 (MBM2)1,400 nMfluorescence polarisation
KMT2A 1-466.8 nMcalorimetry
KMT2A 1-1609.8 nMcalorimetry
KMT2A 1-160 with F9A1,550 nMcalorimetry

Two things fall out of this table. First, Phe9 is the hot spot: a single alanine substitution costs about 160-fold in affinity, which is why the pocket that accepts it is the one the chemistry targets. Second, MBM1 and MBM2 are negatively cooperative, since the full 1-46 fragment binds at 6.8 nM rather than the roughly 3 nM two independent sites would predict.

Structures you can actually load

Every identifier here was resolved against the RCSB API rather than recalled.

  • 4GQ6 menin with KMT2A 6-15, 1.55 Å. The canonical MBM1 complex.
  • 3U85 menin with KMT2A 6-25, 3.0 Å; 3U88 the menin-KMT2A-LEDGF ternary complex, 3.0 Å.
  • 7UJ4 (1.96 Å) and 8E90 (1.85 Å) menin with revumenib.
  • 8VA6 menin with ziftomenib (1.57 Å); 8VA5 the T349M mutant (1.30 Å).
  • 9Z4X menin with bleximenib, 2.95 Å.
  • 9C4S / 9C4T / 9C4U / 9C4V menin-KMT2A with the G331R, M327I, T349M and G331D resistance mutants, 1.46-1.57 Å.

There is no structure of menin bound to MBM2. That motif is defined biochemically only.

A correction worth recording, because it propagates through reviews: 4GQ3 and 4GQ4 are menin with the inhibitors MI-2 and MI-2-2, not with an MBM1 peptide, and they come from Shi et al. in Blood, not from Huang et al. in Nature. 6E1A is menin with compound M-89, not revumenib. There is no AlphaFold model of full-length KMT2A, since at 3,969 residues it exceeds the database's full-chain coverage.

Why this interface is the right first target, and where the argument is thin

It is retained in every KMT2A fusion regardless of partner, it is a compact well-formed pocket rather than a flat surface, it has validated chemical matter with two approved drugs, and blocking it evicts the fusion from chromatin rather than merely slowing it.

The thin part: this pocket is not KMT2A-specific. The same menin cavity binds JUND, with opposite transcriptional output, which is captured structurally in 3U86 2. Anything that fills the pocket also displaces whatever else uses it, and the consequences of blocking menin-JUND have not been worked out.

Update: the JUND question has been answered, and the answer is unwelcome

When this entry was first written it flagged an open question: the menin pocket is not KMT2A-specific, it also binds JUND, and nobody had worked out what displacing JUND does.

It has now been worked out, and the answer is a liability. Menin inhibitors disrupt menin-JUND as well as menin-KMT2A, which increases JUND occupancy on chromatin, upregulates its targets, and contributes to resistance. Removing JUND genetically, or inhibiting JNK pharmacologically, synergises with menin inhibition 4.

This matters beyond one drug. The liberation of a second factor is a consequence of occupying a shared pocket, so it is plausibly intrinsic to this binding site rather than to any particular molecule. Better potency does not fix it. It also suggests a concrete combination: a menin inhibitor plus a JNK inhibitor, which the paper's own data supports.

The practical read for this project: when you drug a pocket that serves two masters, you should expect to find out what the other master does when it is set free.

Facts and figures
partner agene-men1
partner bgene-kmt2a
motif bMBM1, KMT2A aa 4-15, core RWRFP aa 6-10
motif b secondaryMBM2, KMT2A aa 23-40
kd NM53
druggabilityValidated. Deep, well-formed cavity with two approved small-molecule binders and multiple co-crystal structures.
kd measurements
KMT2A 1-466.800KMT2A 1-46: 6.8KMT2A 1-1609.800KMT2A 1-160: 9.8KMT2A 4-15 (MBM1)53.0KMT2A 4-15 (MBM1): 53KMT2A 4-15 (MBM1)72.0KMT2A 4-15 (MBM1): 72KMT2A 23-40 (MBM2)1,400KMT2A 23-40 (MBM2): 1400KMT2A 1-160 F9A1,550KMT2A 1-160 F9A: 1550
hot spot residues
[
  "KMT2A Phe9",
  "KMT2A Pro10",
  "KMT2A Pro13"
]
kd measurements — the numbers behind the chart
[
  {
    "ligand": "KMT2A 4-15 (MBM1)",
    "kd_nM": 53,
    "method": "fluorescence polarisation"
  },
  {
    "ligand": "KMT2A 4-15 (MBM1)",
    "kd_nM": 72,
    "method": "ITC"
  },
  {
    "ligand": "KMT2A 23-40 (MBM2)",
    "kd_nM": 1400,
    "method": "fluorescence polarisation"
  },
  {
    "ligand": "KMT2A 1-46",
    "kd_nM": 6.8,
    "method": "ITC"
  },
  {
    "ligand": "KMT2A 1-160",
    "kd_nM": 9.8,
    "method": "ITC"
  },
  {
    "ligand": "KMT2A 1-160 F9A",
    "kd_nM": 1550,
    "method": "ITC"
  }
]
structures
[
  "4GQ6",
  "3U85",
  "3U88",
  "7UJ4",
  "8E90",
  "8VA6",
  "8VA5",
  "9Z4X",
  "9C4S",
  "9C4T",
  "9C4U",
  "9C4V"
]
ligands
[
  "drug-revumenib",
  "drug-ziftomenib",
  "drug-bleximenib"
]
ID corrections
[
  "4GQ3 and 4GQ4 are menin with MI-2 and MI-2-2 inhibitors, not MBM1 peptide complexes, and are from Shi et al. Blood 2012 rather than Huang et al. Nature 2012",
  "6E1A is menin with compound M-89, not revumenib",
  "No AlphaFold model exists for full-length KMT2A (AF-Q03164-F1 returns 404)"
]
menin mbm1 kd conditions
{
  "_why": "Added by king sweep 2026-09-21 (Q82 corrections-owed #3). This entry quotes the menin-MBM1 53 nM figure. That number is NOT comparable to the KMT2A CXXC-DNA affinities without stating its buffer, and the omission is how a 1,300-fold 'discrepancy' was manufactured.",
  "value": "53 nM",
  "motif": "KMT2A MBM1, residues 4-15, FITC-labelled peptide at 15 nM",
  "method": "fluorescence polarisation",
  "buffer": "50 mM Tris, pH 7.5, 50 mM NaCl, 1 mM DTT",
  "nacl_mM": 50,
  "companion_itc": "72 nM by ITC, 50 mM phosphate pH 7.5, 50 mM NaCl, 1 mM beta-mercaptoethanol, 27 C",
  "source_pmid": "20961854",
  "source_quote": "\"in the FP buffer (50 mM Tris, pH 7.5, 50 mM NaCl, 1 mM DTT) used for binding experiments (Kd measurements)\" -- Grembecka 2010 JBC, Methods, fetched and read from PMC3003368 on 2026-09-21",
  "do_not_compare_naively": {
    "against": "KMT2A CXXC-DNA Kd 44 uM (PMID 20010842, Cierpicki 2010)",
    "because": "that measurement was made at 300 mM NaCl -- verbatim from its Methods, \"50 mM phosphate buffer (pH 7.1), 300 mM NaCl, 2 mM DTT at 25 C\" (PMC2908503, read 2026-09-21) -- SIX-FOLD more salt, on a salt-sensitive protein-DNA contact, against a hydrophobic peptide pocket that is not.",
    "best_matched_pair": "44 uM at 300 mM NaCl vs the 5.7 uM tagless CXXC measurement at 150 mM NaCl gives 108-fold against menin, not ~1,000-fold",
    "see": "ana-the-menin-affinity-comparison-was-made-at-one-sixth-the-salt"
  },
  "added": "2026-09-21"
}
cxxc dna kd conditions
{
  "_why": "Added by king sweep 2026-09-21 (cycle 46). This entry quotes the KMT2A CXXC-DNA 44 uM. That number is a property of five choices, not of the molecule, and quoting it bare is how this graph manufactured a 1,300-fold 'discrepancy' with the menin contact.",
  "value": "44 uM",
  "construct": "isolated CXXC domain, KMT2A 1147-1203, untagged, 15N-labelled",
  "ligand": "DNA pal oligonucleotide, one CpG element",
  "method": "NMR titration",
  "buffer": "50 mM phosphate, pH 7.1, 300 mM NaCl, 2 mM DTT, 25 C",
  "nacl_mM": 300,
  "source_pmid": "20010842",
  "source_quote": "\"Determination of the dissociation constants by NMR for the CXXC domain (MLL 1147-1203) and mutants was performed by titration of 15N-labeled protein with concentrated solutions of DNA pal oligonucleotide. Experiments were carried out in 50 mM phosphate buffer (pH 7.1), 300 mM NaCl, 2 mM DTT at 25 C.\" -- Cierpicki 2010 NSMB, Methods, fetched and read from PMC2908503 on 2026-09-21. The result sentence reads \"The wild type protein yielded a Kd of 44 uM\".",
  "this_is_the_high_salt_end": "300 mM NaCl is roughly twice physiological ionic strength and SIX TIMES the 50 mM the menin-MBM1 53 nM was measured in. The same domain measured tagless at 150 mM NaCl gives 5.7 uM -- 7.7-fold tighter from salt alone.",
  "do_not_compare_naively": {
    "against": "menin-MBM1 53 nM (PMID 20961854), measured at 50 mM NaCl by FP",
    "best_matched_pair": "108-fold, not ~1,000-fold",
    "see": "ana-the-menin-affinity-comparison-was-made-at-one-sixth-the-salt"
  },
  "added": "2026-09-21"
}
How this could bite us back
  • The pocket is shared with JUND and is not KMT2A-specific, so selectivity comes from the cell's dependency rather than from the chemistry.
  • Resistance mutations in this exact interface are already documented in patients and leave the natural KMT2A interaction intact.
  • The pocket serves two masters: blocking it frees JUND onto chromatin and that liberation itself drives resistance, which is plausibly intrinsic to the binding site rather than to any one compound.
Still open
  1. Does JUND liberation contribute to resistance in treated children, or only in cell lines and xenografts? The clinical version of this question is untested.
  2. Does the fusion protein's avidity on chromatin, from CXXC-DNA binding plus LEDGF, mean the effective affinity in a cell is far tighter than the 53 nM measured for a peptide, and is that a ceiling no potency can fix?
  3. Is there a druggable pocket unique to the fusion junction itself, which would be selective in a way this shared pocket can never be?
  4. Do the different menin inhibitors differ in how much JUND they liberate? If so, that is a selection criterion nobody is currently applying.
  5. Revumenib selects MEN1 mutations in 39% of relapses but ziftomenib and bleximenib apparently do not. Is that a real difference in selective pressure, or shorter follow-up and smaller treated numbers?
  6. Verify the quantitative claims in E1 (Kd 53 nM by fluorescence polarisation, 72 nM by calorimetry, MBM2 about 1,400 nM, Phe9 about 160-fold, negative cooperativity) against the full text of PMID 20961854: its abstract (re-read 2026-10-14) supports only a two-motif fragment Kd of about 10 nM, MBM1 as the high-affinity motif, and Phe9, Pro10 and Pro13 as critical. The full text could not be retrieved on 2026-10-14 (Europe PMC server error; PMC E-utilities returned front matter only).
Every source behind this entry (4)
  1. E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    KMT2A MBM1 (residues 4-15, core RWRFP at 6-10) binds menin with Kd 53 nM by fluorescence polarisation and 72 nM by calorimetry; MBM2 (residues 23-40) binds at about 1,400 nM; Phe9 is a hot spot whose mutation costs roughly 160-fold; MBM1 and MBM2 are negatively cooperative.

    Molecular basis of the mixed lineage leukemia-menin interaction: implications for targeting mixed lineage leukemias · Grembecka J, Belcher AM, Hartley T, Cierpicki T · Journal of Biological Chemistry 2010
    PMID 20961854DOI
    What this evidence cannot show

    Affinities are for isolated synthetic peptides against recombinant menin in vitro, not for the full fusion protein on chromatin, where avidity from CXXC-DNA binding and LEDGF contacts will dominate. Calorimetry and fluorescence polarisation values differ by roughly 35% for the same peptide, which sets the realistic precision. Citation correction 2026-09-19: the title field previously read 'Menin-MLL inhibitors reverse oncogenic activity of MLL fusion proteins in leukemia (and the associated menin-binding-motif characterisation)'. That is a descriptive composite, not a title, and it leads with the exact title of a DIFFERENT real paper. The PMID and DOI were always correct and match the claim; only the title field was wrong. Three other entries cite the same PMID under its correct title, so this was isolated to this entry.

    Evidence that argues against this (2)
    • A 53 nM grip that drugs demonstrably break is not the same as a grip that matters once broken. In the only human sample profiled under revumenib, the oncoprotein AND menin fell to UNDETECTABLE while ENL persisted at oncoprotein target loci - the interface was fully disengaged and the programme kept running. That is worse for the hypothesis than a resistance mutation, which at least concedes the target still matters. Nature Communications 2024
    • The clinical ceiling argues the same way from the other end. In AUGMENT-101 phase 2, blocking this interface with revumenib produced CR+CRh in 22.8% of 57 efficacy-evaluable patients. Overall response was 63.2%, so the pocket is plainly engaged and the biology plainly moves - but under a quarter reach the endpoint that matters, in a disease where the interface is supposed to be the dependency. Journal of Clinical Oncology 2025
  2. E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    The same menin pocket that binds the KMT2A MBM1 motif also binds JUND, with opposite transcriptional consequences, so the pocket is not KMT2A-selective.

    PMID 22327296DOI
    What this evidence cannot show

    Structural and biochemical work; the in vivo consequence of displacing JUND with a menin inhibitor in a patient has not been measured.

    Evidence that argues against this (1)
    • The shared-pocket objection predicts on-target harm from displacing menin's other partners, and that prediction has not been borne out in the way it was feared. Revumenib was approved on this cohort with a toxicity profile dominated by differentiation syndrome and QT prolongation (grade 3/4 QT 12%) - mechanism-linked and manageable - rather than by the consequences of displacing JUND or menin's tumour-suppressor functions. A non-selective pocket has proved more tolerable than its non-selectivity predicted. Annals of Pharmacotherapy 2025
  3. E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Structures of menin with revumenib (7UJ4, 8E90) and with menin interface resistance mutants show that the mutations impair inhibitor binding while preserving MLL1 binding.

    MEN1 mutations mediate clinical resistance to menin inhibition · Perner F, Stein EM, Wenge DV, et al. · Nature 2023
    PMID 36922589DOI
    What this evidence cannot show

    Structures are of menin fragments with peptides and small molecules, not of an intact fusion protein engaged with chromatin.

    Evidence that argues against this (2)
    • Interface resistance mutations are not the class-wide dead end this framing suggests. The mutants selected by revumenib are not uniformly cross-resistant: ziftomenib retained antileukaemic activity against T349M and low-nanomolar potency against G331R. The interface can survive a mutation that defeats one ligand, which argues the pocket is a more durable target than a single drug's resistance spectrum implies. Blood 2026
    • And MEN1 mutation is not the only route out. TP53 inactivation confers de novo revumenib resistance with impaired induction of TP53 targets and deregulated BCL-2/BH3 proteins - resistance that never touches the interface at all, so no amount of interface engineering addresses it. CAVEAT: this is a bioRxiv PREPRINT and has not been peer reviewed. bioRxiv (PREPRINT, not peer reviewed) 2025
  4. E4strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper

    Menin inhibitors also disrupt the menin-JUND interaction, increasing JUND occupancy on chromatin and upregulating its target genes, which contributes to resistance; inactivating JUND or inhibiting JNK synergises with menin inhibition.

    PMID 42371796DOI
    What this evidence cannot show

    Cell lines and immunocompromised mouse xenografts, not patients. Whether JUND liberation contributes to clinical resistance in treated children is untested. One author is employed by the drug's sponsor, which is disclosed rather than disqualifying.

    Evidence that argues against this (1)
    • The JUND resistance mechanism is demonstrated in cell lines and xenografts; the clinically documented route is a different one. Acquired MEN1 mutations were described in 39% of post-revumenib relapses, and notably have NOT been identified following ziftomenib or bleximenib. Whether JUND liberation contributes measurably in treated patients, and whether it differs across the class, is untested - so this should not yet displace MEN1 mutation as the resistance mechanism to design against. Hematology Am Soc Hematol Educ Program 2025
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