Analysis (runnable): can a menin ligand tell KMT2A from JUND? A structural and co-folding selectivity profile of the whole inhibitor class

[
  "PDB entries for menin complexes: 3U85, 3U88, 4GQ6, 7UJ4, 8E90, 8VA6, 8VA5, 9Z4X, 9C4S-9C4V",
  "UniProt O00255 (menin), Q03164 (KMT2A) and P17535 (JUND) sequences",
  "SMILES for revumenib (CHEMBL4650827), ziftomenib, bleximenib, enzomenib and icovamenib from ChEMBL",
  "Reported class differences in MEN1 mutation rate, hyperparathyroidism and differentiation syndrome from labels and PMID 41347983"
]

[
  "per-residue contact maps and buried-surface comparison for menin-MLL1 versus menin-JUND",
  "list of residues or sub-pockets contacted by one partner and not the other, or an explicit statement that none exist",
  "Boltz co-folding scores and a predicted per-compound displacement ranking for each partner",
  "concordance table against observed class differences",
  "a one-page specification for the two-peptide fluorescence-polarisation counter-screen"
]

[
  "hyp-partner-selective-menin-ligand-separates-mandates"
]

{
  "_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"
}

{
  "_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"
}