// NMR / fragment screening · Protein pipeline, Phase 6 evidence layer

FKBP12

108 aa (P62942) · 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 1FKJ (FK506-bound — the textbook NMR/fragment-screening pocket). The real pocket (His87 and Ile91 match exactly, several adjacent loop residues close) shows up at rank 2 (persistence 0.6), not rank 1 — rank 1 is a different region near the N-terminus. This was the batch's own designated sanity anchor; the correct answer is present, just demoted. Structural check: CA RMSD vs. 1FKJ is 0.53 Å whole-chain, 0.57 Å within the pocket — near-experimental accuracy on this small, single-domain target.

Rank 1 Rank 2 Rank 3

// Sequence

MGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

Length108 aa

UniProtP62942

Mean structure confidence0.9627

Pocket clusters3

Numbering cross-walk107/108 vs. 2PPN

// Findings

Family, precedent, and provenance

Family classification

returned data

FKBP_C (PF00254) — FKBP-type peptidyl-prolyl cis-trans isomerase

E=4.30e-37 · bit score 127.0 · passes GA threshold: yes

Known ligand precedent

returned data

439 total structures in family · 8 distinct ligand scaffolds curated

7AOT — RTQ
7APW — RSB
8R5K — Y6Z
7APS — RR5
6TX6 — NCA

Conservation

returned data

126 seed sequences · mean pairwise identity 31.4%

Similar known proteins

returned data

8X6P — 100.0% identity · (none)
2PPN — 98.1% identity · (none)
6YF3 — 97.2% identity · CD, OOZ
6YF2 — 97.2% identity · CD, OP5
6YF1 — 97.2% identity · OP8

Structure-based (Foldseek)

4N19 — TM 1.000 · 98% id
8PPZ — TM 1.000 · 99% id (new vs. sequence list)
4IPX — TM 1.000 · 98% id (new vs. sequence list)
6M4W — TM 1.000 · 100% id (new vs. sequence list)
8VK3 — TM 0.999 · 97% id (new vs. sequence list)

Interaction fingerprints (Evidence Integration Layer)

returned data

Representative complex: 6YF3 (OOZ, 1.00 Å)

Residue (PDB)	Residue (pipeline)	Interaction	Partner
37	38	hydrogen bond	ASP37 (hydrogen bond) with ligand OOZ
54	55	hydrogen bond	GLU54 (hydrogen bond) with ligand OOZ
56	57	hydrogen bond	ILE56 (hydrogen bond) with ligand OOZ
26	27	hydrophobic	TYR26 (hydrophobic) with ligand OOZ
36	37	hydrophobic	PHE36 (hydrophobic) with ligand OOZ
46	47	hydrophobic	PHE46 (hydrophobic) with ligand OOZ
46	47	hydrophobic	PHE46 (hydrophobic) with ligand OOZ
56	57	hydrophobic	ILE56 (hydrophobic) with ligand OOZ
59	60	hydrophobic	TRP59 (hydrophobic) with ligand OOZ
90	91	hydrophobic	ILE90 (hydrophobic) with ligand OOZ
46	47	hydrophobic	PHE46 (hydrophobic) with ligand OOZ
59	60	hydrophobic	TRP59 (hydrophobic) with ligand OOZ

Representative complex: 6YF2 (OP5, 1.03 Å)

Residue (PDB)	Residue (pipeline)	Interaction	Partner
37	38	hydrogen bond	ASP37 (hydrogen bond) with ligand OP5
54	55	hydrogen bond	GLU54 (hydrogen bond) with ligand OP5
56	57	hydrogen bond	ILE56 (hydrogen bond) with ligand OP5
26	27	hydrophobic	TYR26 (hydrophobic) with ligand OP5
46	47	hydrophobic	PHE46 (hydrophobic) with ligand OP5
46	47	hydrophobic	PHE46 (hydrophobic) with ligand OP5
46	47	hydrophobic	PHE46 (hydrophobic) with ligand OP5
56	57	hydrophobic	ILE56 (hydrophobic) with ligand OP5
59	60	hydrophobic	TRP59 (hydrophobic) with ligand OP5
59	60	hydrophobic	TRP59 (hydrophobic) with ligand OP5
82	83	hydrophobic	TYR82 (hydrophobic) with ligand OP5
91	92	hydrophobic	ILE91 (hydrophobic) with ligand OP5

Representative complex: 6YF1 (OP8, 1.12 Å)

Residue (PDB)	Residue (pipeline)	Interaction	Partner
37	38	hydrogen bond	ASP37 (hydrogen bond) with ligand OP8
26	27	hydrogen bond	TYR26 (hydrogen bond) with ligand OP8
82	83	hydrogen bond	TYR82 (hydrogen bond) with ligand OP8
56	57	hydrogen bond	ILE56 (hydrogen bond) with ligand OP8
26	27	hydrophobic	TYR26 (hydrophobic) with ligand OP8
36	37	hydrophobic	PHE36 (hydrophobic) with ligand OP8
46	47	hydrophobic	PHE46 (hydrophobic) with ligand OP8
55	56	hydrophobic	VAL55 (hydrophobic) with ligand OP8
56	57	hydrophobic	ILE56 (hydrophobic) with ligand OP8
59	60	hydrophobic	TRP59 (hydrophobic) with ligand OP8
91	92	hydrophobic	ILE91 (hydrophobic) with ligand OP8
46	47	hydrophobic	PHE46 (hydrophobic) with ligand OP8
59	60	hydrophobic	TRP59 (hydrophobic) with ligand OP8
82	83	hydrophobic	TYR82 (hydrophobic) with ligand OP8
85	86	water bridge	THR85 (water bridge) with ligand OP8

Structural analysis — ranked pocket clusters

returned data

Residue numbers below are pipeline-sequential, with the literature (author-deposited PDB 2PPN) number shown in parentheses — 107/108 residues cross-walked.

Rank	Persistence	Residues
#1	0.8	1(?), 2(1), 3(2), 4(3), 32(31), 76(75), 78(77), 79(78), 97(96)
#2	0.6	31(30), 35(34), 86(85), 88(87), 89(88), 90(89), 91(90), 92(91), 93(92), 94(93)
#3	0.8	19(18), 51(50), 52(51), 53(52), 54(53), 61(60), 62(61), 65(64)

Pocket residues overlapping known interaction sites

Pocket 1: no overlap with known interaction sites (9 checked)
Pocket 2: residues 86, 91, 92 (3 of 10 pocket residues match a known interaction site)
Pocket 3: no overlap with known interaction sites (8 checked)

Pocket functional context (UniProt + ClinVar)

Pocket 1

no UniProt functional features or ClinVar variants overlap with pocket residues

Pocket 2

no UniProt functional features or ClinVar variants overlap with pocket residues

Pocket 3

Residue 53: Modified residue — N6-acetyllysine; alternate
Residue 53: Modified residue — N6-succinyllysine; alternate

// Limitations & data provenance

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

Family classificationreturned data

Known ligand precedentreturned data

Interaction fingerprintsreturned data

Functional contextreturned data

Conservationreturned data

Structural analysisreturned data

Similar known proteinsreturned data

Download PDF report ← All demos