// Small-molecule med chem · Protein pipeline, Phase 6 evidence layer

MDM2

491 aa (Q00987) · predicted structure regenerated live for this page (AlphaFold DB + ANM ensemble + fpocket + cross-frame ranker, same pipeline as every worked example on this site).

// Independently verified against a real PDB structure — not pipeline output

Independently checked against PDB 1YCR (MDM2 + p53 transactivation peptide, the structure that defined the nutlin-class inhibitor pocket). The rank-1 cluster (persistence 1.0) exactly matches 8 of 22 real p53-contact residues — 25, 26, 50, 51, 94, 96, 100, 104 — landing precisely on the real, druggable PPI cleft. Structural check: CA RMSD vs. 1YCR is 0.49 Å whole-domain, 0.61 Å within the pocket residues specifically — near-experimental accuracy on the resolved N-terminal domain.

Rank 1 Rank 2 Rank 3

// Sequence

MCNTNMSVPTDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSENRCHLEGGSDQKDLVQELQEEKPSSSHLVSRPSTSSRRRAISETEENSDELSGERQRKRHKSDSISLSFDESLALCVIREICCERSSSSESTGTPSNPDLDAGVSEHSGDWLDQDSVSDQFSVEFEVESLDSEDYSLSEEGQELSDEDDEVYQVTVYQAGESDTDSFEEDPEISLADYWKCTSCNEMNPPLPSHCNRCWALRENWLPEDKGKDKGEISEKAKLENSTQAEEGFDVPDCKKTIVNDSRESCVEENDDKITQASQSQESEDYSQPSTSSSIIYSSQEDVKEFEREETQDKEESVESSLPLNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYFP
Length491 aa
UniProtQ00987
Mean structure confidence0.6258
Pocket clusters3
Numbering cross-walk94/491 vs. 6Q9L

// Confidence flags — rules-based, no learned calibration

cautionNumbering cross-walk against 6Q9L only mapped 94/491 residues (19%) — the reference structure found is a poor match for most of this sequence (e.g. a short peptide/fragment, or a construct covering only a small domain of a larger protein). Most residues will show as unmapped ('?'); treat any '(literature)' number that DOES appear as coincidental unless independently checked, not as evidence the cross-walk is reliable for this target.

// Findings

Family, precedent, and provenance

Family classification

returned data

zf-C3HC4_3 (PF13920) — Zinc finger, C3HC4 type (RING finger)

E=1.10e-10 · bit score 41.9 · passes GA threshold: yes

Known ligand precedent

returned data

74 total structures in family · 8 distinct ligand scaffolds curated

  • 13SY — W2J
  • 13SQ — U0P
  • 13SL — JHP
  • 13ST — A1H9V
  • 13SW — A1AJM

Conservation

returned data

309 seed sequences · mean pairwise identity 29.4%

Similar known proteins

returned data
  • 3T6P — 4.4% identity · (none)
  • 9SA1 — 0.0% identity · (none)
  • 9SA2 — 0.0% identity · (none)
  • 6SQP — 0.0% identity · (none)
  • 13SY — 0.0% identity · W2J

Structure-based (Foldseek)

  • 4HFZ — TM 1.000 · 98% id (new vs. sequence list)
  • 3LNZ — TM 1.000 · 100% id (new vs. sequence list)
  • 3TPX — TM 1.000 · 100% id (new vs. sequence list)
  • 5UMM — TM 1.000 · 100% id (new vs. sequence list)
  • 3IWY — TM 1.000 · 100% id (new vs. sequence list)

Interaction fingerprints (Evidence Integration Layer)

no_ligand_bound_structure

8 ligand-bound structure(s) exist for this target's Pfam family (PF13920), but none checked aligned to the query at >=50% sequence coverage — likely other members of the same broad family (e.g. related kinases), not this specific protein. Interaction fingerprints require a structure of the query protein itself.

Structural analysis — ranked pocket clusters

returned data

Residue numbers below are pipeline-sequential, with the literature (author-deposited PDB 6Q9L) number shown in parentheses — 94/491 residues cross-walked.

RankPersistenceResidues
#1123(23), 24(24), 25(25), 26(26), 49(49), 50(50), 51(51), 94(94), 95(95), 96(96), 97(97), 98(98), 100(100), 101(101), 104(104), 190(?), 191(?), 192(?), 193(?), 194(?) …
#21263(?), 266(?), 268(?), 270(?), 271(?), 272(?), 273(?), 274(?), 275(?), 276(?), 462(?), 463(?), 466(?), 467(?), 469(?), 470(?), 484(?), 485(?), 486(?), 487(?) …
#31275(?), 276(?), 277(?), 278(?), 279(?), 280(?), 282(?), 428(?), 429(?), 430(?), 431(?), 449(?), 458(?), 486(?), 487(?), 488(?), 489(?), 490(?), 491(?)

Pocket functional context (UniProt + ClinVar)

Pocket 1

  • Residue 23: Region — Necessary for interaction with USP2
  • Residue 23: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 24: Region — Necessary for interaction with USP2
  • Residue 24: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 25: Region — Necessary for interaction with USP2
  • Residue 25: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 26: Region — Necessary for interaction with USP2
  • Residue 26: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 49: Region — Necessary for interaction with USP2
  • Residue 49: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 50: Region — Necessary for interaction with USP2
  • Residue 50: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 51: Region — Necessary for interaction with USP2
  • Residue 51: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 94: Region — Necessary for interaction with USP2
  • Residue 94: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 95: Region — Necessary for interaction with USP2
  • Residue 95: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 96: Region — Necessary for interaction with USP2
  • Residue 96: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 97: Region — Necessary for interaction with USP2
  • Residue 97: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 98: Region — Necessary for interaction with USP2
  • Residue 98: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 100: Region — Necessary for interaction with USP2
  • Residue 100: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 101: Region — Necessary for interaction with USP2
  • Residue 101: Region — Sufficient to promote the mitochondrial pathway of apoptosis
  • Residue 104: Region — Necessary for interaction with USP2
  • Residue 190: Region — Interaction with PYHIN1 and necessary for interaction with RFFL and RNF34
  • Residue 190: Region — Interaction with MTBP
  • Residue 190: Modified residue — Phosphoserine
  • Residue 191: Region — Interaction with PYHIN1 and necessary for interaction with RFFL and RNF34
  • Residue 191: Region — Interaction with MTBP
  • Residue 192: Region — Interaction with PYHIN1 and necessary for interaction with RFFL and RNF34
  • Residue 192: Region — Interaction with MTBP
  • Residue 193: Region — Interaction with PYHIN1 and necessary for interaction with RFFL and RNF34
  • Residue 193: Region — Interaction with MTBP
  • Residue 194: Region — Interaction with PYHIN1 and necessary for interaction with RFFL and RNF34
  • Residue 194: Region — Interaction with MTBP
  • Residue 195: Region — Interaction with PYHIN1 and necessary for interaction with RFFL and RNF34
  • Residue 195: Region — Interaction with MTBP
  • Residue 196: Region — Interaction with PYHIN1 and necessary for interaction with RFFL and RNF34
  • Residue 196: Region — Interaction with MTBP
  • Residue 197: Region — Interaction with PYHIN1 and necessary for interaction with RFFL and RNF34
  • Residue 197: Region — Interaction with MTBP
  • Residue 198: Region — Interaction with PYHIN1 and necessary for interaction with RFFL and RNF34
  • Residue 198: Region — Interaction with MTBP

Pocket 2

  • Residue 263: Region — Interaction with MTBP
  • Residue 263: Region — Mediates interaction with RAD54B
  • Residue 263: Region — ARF-binding
  • Residue 263: Region — Region II
  • Residue 263: Region — Disordered
  • Residue 266: Region — Interaction with MTBP
  • Residue 266: Region — Mediates interaction with RAD54B
  • Residue 266: Region — ARF-binding
  • Residue 266: Region — Region II
  • Residue 266: Region — Disordered
  • Residue 268: Region — Interaction with MTBP
  • Residue 268: Region — Mediates interaction with RAD54B
  • Residue 268: Region — ARF-binding
  • Residue 268: Region — Region II
  • Residue 268: Region — Disordered
  • Residue 270: Region — Interaction with MTBP
  • Residue 270: Region — Mediates interaction with RAD54B
  • Residue 270: Region — ARF-binding
  • Residue 270: Region — Region II
  • Residue 270: Region — Disordered
  • Residue 271: Region — Interaction with MTBP
  • Residue 271: Region — Mediates interaction with RAD54B
  • Residue 271: Region — ARF-binding
  • Residue 271: Region — Region II
  • Residue 271: Region — Disordered
  • Residue 272: Region — Interaction with MTBP
  • Residue 272: Region — Mediates interaction with RAD54B
  • Residue 272: Region — ARF-binding
  • Residue 272: Region — Region II
  • Residue 272: Region — Disordered
  • Residue 273: Region — Interaction with MTBP
  • Residue 273: Region — Mediates interaction with RAD54B
  • Residue 273: Region — ARF-binding
  • Residue 273: Region — Region II
  • Residue 273: Region — Disordered
  • Residue 274: Region — Interaction with MTBP
  • Residue 274: Region — Mediates interaction with RAD54B
  • Residue 274: Region — ARF-binding
  • Residue 274: Region — Region II
  • Residue 274: Region — Disordered
  • Residue 275: Region — Interaction with MTBP
  • Residue 275: Region — Mediates interaction with RAD54B
  • Residue 275: Region — ARF-binding
  • Residue 275: Region — Region II
  • Residue 276: Region — Interaction with MTBP
  • Residue 276: Region — Mediates interaction with RAD54B
  • Residue 276: Region — ARF-binding
  • Residue 276: Region — Region II
  • Residue 276: Region — Necessary for interaction with USP2
  • Residue 462: Region — Necessary for interaction with USP2
  • Residue 463: Region — Necessary for interaction with USP2
  • Residue 466: Region — Necessary for interaction with USP2
  • Residue 467: Region — Necessary for interaction with USP2
  • Residue 469: Region — Necessary for interaction with USP2
  • Residue 470: Region — Necessary for interaction with USP2
  • Residue 484: Region — Necessary for interaction with USP2
  • Residue 485: Region — Necessary for interaction with USP2
  • Residue 486: Region — Necessary for interaction with USP2
  • Residue 487: Region — Necessary for interaction with USP2
  • Residue 489: Region — Necessary for interaction with USP2

Pocket 3

  • Residue 275: Region — Interaction with MTBP
  • Residue 275: Region — Mediates interaction with RAD54B
  • Residue 275: Region — ARF-binding
  • Residue 275: Region — Region II
  • Residue 276: Region — Interaction with MTBP
  • Residue 276: Region — Mediates interaction with RAD54B
  • Residue 276: Region — ARF-binding
  • Residue 276: Region — Region II
  • Residue 276: Region — Necessary for interaction with USP2
  • Residue 277: Region — Interaction with MTBP
  • Residue 277: Region — Mediates interaction with RAD54B
  • Residue 277: Region — ARF-binding
  • Residue 277: Region — Region II
  • Residue 277: Region — Necessary for interaction with USP2
  • Residue 278: Region — Interaction with MTBP
  • Residue 278: Region — Mediates interaction with RAD54B
  • Residue 278: Region — ARF-binding
  • Residue 278: Region — Region II
  • Residue 278: Region — Necessary for interaction with USP2
  • Residue 279: Region — Interaction with MTBP
  • Residue 279: Region — Mediates interaction with RAD54B
  • Residue 279: Region — ARF-binding
  • Residue 279: Region — Region II
  • Residue 279: Region — Necessary for interaction with USP2
  • Residue 280: Region — Interaction with MTBP
  • Residue 280: Region — Mediates interaction with RAD54B
  • Residue 280: Region — ARF-binding
  • Residue 280: Region — Region II
  • Residue 280: Region — Necessary for interaction with USP2
  • Residue 282: Region — Interaction with MTBP
  • Residue 282: Region — Mediates interaction with RAD54B
  • Residue 282: Region — ARF-binding
  • Residue 282: Region — Region II
  • Residue 282: Region — Necessary for interaction with USP2
  • Residue 428: Region — Necessary for interaction with USP2
  • Residue 429: Region — Necessary for interaction with USP2
  • Residue 429: Modified residue — Phosphoserine; by ATM
  • Residue 430: Region — Necessary for interaction with USP2
  • Residue 431: Region — Necessary for interaction with USP2
  • Residue 449: Region — Necessary for interaction with USP2
  • Residue 458: Region — Necessary for interaction with USP2
  • Residue 486: Region — Necessary for interaction with USP2
  • Residue 487: Region — Necessary for interaction with USP2
  • Residue 488: Region — Necessary for interaction with USP2
  • Residue 489: Region — Necessary for interaction with USP2
  • Residue 490: Region — Necessary for interaction with USP2
  • Residue 491: Region — Necessary for interaction with USP2

// Limitations & data provenance

Auto-populated from each section’s own status — not hand-maintained.

Family classificationreturned data
Known ligand precedentreturned data
Interaction fingerprintsno_ligand_bound_structure
Functional contextreturned data
Conservationreturned data
Structural analysisreturned data
Similar known proteinsreturned data
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