KpKP13 Protein target profile

Cobalt-precorrin-8X methylmutase

Accession: KP13_02326

Gene: AHE42896.1 cbiC 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSI6

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Length 211

Pocket druggability (P2Rank · AlphaFold DB model) 0.056

Direct ligand evidence 0 55 total records

Functional annotation 0 EC 2 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Risks to review

Microbiome similarity 121 of 4744 screened genomes (2.6%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.37. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.06.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: No hit
Gut microbiome similarity: 2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 97.12 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.056

Structure A0A0H3GSI6

Pocket Pocket 1

Druggability (FPocket) 0.374

Structure A0A0H3GSI6

Pocket Pocket 3

ColabFold model

P2Rank 0.069 · Pocket 1

FPocket 0.345 · Pocket 7

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 121 / 4744 genomes with a hit

Prevalence 2.6%

Sequence

Primary amino-acid sequence viewer.

MQYIQQPQAIEAKSFDIISEIIAETRPDYRFASPLHEAIIKRVIHTTADFDWLDILWFSPDALIALSEALSRPCTLYTDTTMALSGINKTLLARFGGECRCYISDPRVVREAQSRGMTRSMAAVDIAVQEPGEKVFVFGNAPTALFRLLEHRETAIGGVVGVPVGFVGAAESKAALSESGLPAIAALGRKGGSNVAAAIVNALLYHLREAQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization: Unknown

Gene Ontology (GO)

GO:0016993 Catalysis of the reaction: precorrin-8X = hydrogenobyrinate.
GO:0009236 The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

7 records

Show feature table

Start	End	DB	Term	Name
10	205	Pfam	PF02570	Precorrin-8X methylmutase
10	205	InterPro	IPR003722	Cobalamin biosynthesis precorrin-8X methylmutase CobH/CbiC
9	209	SUPERFAMILY	SSF63965	Precorrin-8X methylmutase CbiC/CobH
9	209	InterPro	IPR036588	Precorrin-8X methylmutase CobH/CbiC superfamily
1	209	PANTHER	PTHR43588	COBALT-PRECORRIN-8 METHYLMUTASE
1	206	Gene3D	G3DSA:3.40.50.10230	-
1	206	InterPro	IPR036588	Precorrin-8X methylmutase CobH/CbiC superfamily

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.

'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.

'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.056

Likely same site as FPocket 2 2.6 Å 8 shared residues 80% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.007

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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #3

0.374 Unusual size

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Surrounding area

Pocket 2 FPocket #2

0.216

Likely same site as P2Rank 1 2.6 Å 8 shared residues 80% of smaller site

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Surrounding area

All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold DB AF_A0A0H3GSI6	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02326	ColabFold	—	—	full sequence	—	Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

55 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

0UK PDB via homolog 883.0 Da · LogP 5.65 · TPSA 310.2 Open detail RCSB PDB

8F5 PDB via homolog Detail RCSB PDB

COJ PDB via homolog Detail RCSB PDB

P33 PDB via homolog Detail RCSB PDB

P8X PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
0UK RCSB PDB	4FDV	D5AV08	883.0 Da LogP 5.65 TPSA 310.2	4 viol.	✓ Clean	`C[C@@H]1[C@@H]2[C@@H](C(/C(=C/C3=N/C(=C(\C4=N[C…`
8F5 RCSB PDB	5N0G	D5AV08	907.0 Da LogP 6.48 TPSA 310.2	4 viol.	✓ Clean	`C[C@@H]1C2=C(C(C(=N2)/C=C\3/[C@H]([C@](C(=N3)/C…`
COJ RCSB PDB	1I1H	P21638	881.0 Da LogP 5.92 TPSA 310.2	4 viol.	✓ Clean	`C/C/1=C/2\[C@H]([C@]([C@@](N2)([C@H]3[C@@H]([C@…`
P33 RCSB PDB	2AFV	Q8EXP7	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`C(COCCOCCOCCOCCOCCOCCO)O`
P8X RCSB PDB	4AU1	D5AV08	867.0 Da LogP 5.53 TPSA 310.2	4 viol.	✓ Clean	`C[C@@H]1C2=C(C(C(=N2)/C=C\3/[C@H]([C@](C(=N3)/C…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC12501520 ZINC	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716 ZINC	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769 ZINC	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548 ZINC	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829 ZINC	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830 ZINC	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC115086873 ZINC	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264 ZINC	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823 ZINC	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442 ZINC	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710 ZINC	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161 ZINC	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118 ZINC	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257 ZINC	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028 ZINC	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057 ZINC	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776 ZINC	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654 ZINC	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157 ZINC	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059 ZINC	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101 ZINC	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743 ZINC	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860 ZINC	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917 ZINC	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182 ZINC	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921 ZINC	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446 ZINC	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447 ZINC	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC144169243 ZINC	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716 ZINC	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC575441396 ZINC	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC1644613 ZINC	0.611	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC258839852 ZINC	0.611	276.3 Da LogP 0.61 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCC(F)(F)F`
ZINC167715346 ZINC	0.600	266.3 Da LogP -0.18 TPSA 77.4	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCOCCCO`
ZINC34160867 ZINC	0.600	222.3 Da LogP -0.20 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCCO`
ZINC1580159 ZINC	0.588	210.3 Da LogP -0.26 TPSA 58.9	✓ Ro5	✓ Clean	`OCCOCCSCCOCCO`
ZINC142610155 ZINC	0.579	340.4 Da LogP -0.84 TPSA 112.9	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCOCCOCCO`
ZINC1542984426 ZINC	0.579	428.5 Da LogP -0.80 TPSA 131.4	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1542984432 ZINC	0.579	398.4 Da LogP -0.43 TPSA 122.1	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC207588231 ZINC	0.579	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`CNCCOCCOCCOCCO`
ZINC258828116 ZINC	0.579	452.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC258836919 ZINC	0.579	364.4 Da LogP -0.27 TPSA 84.8	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC33967025 ZINC	0.579	252.3 Da LogP -0.87 TPSA 94.5	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCO`
ZINC39267847 ZINC	0.579	208.2 Da LogP -0.89 TPSA 85.2	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCO`
ZINC575440725 ZINC	0.579	295.4 Da LogP -1.03 TPSA 80.6	✓ Ro5	✓ Clean	`CN(CCOCCOCCO)CCOCCOCCO`
ZINC83254087 ZINC	0.579	266.3 Da LogP -0.48 TPSA 94.5	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCO`
ZINC95920522 ZINC	0.579	296.3 Da LogP -0.85 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCOCCO`
ZINC96503406 ZINC	0.579	276.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCO`
ZINC96503425 ZINC	0.579	222.2 Da LogP -0.50 TPSA 85.2	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCO`
ZINC96503526 ZINC	0.579	442.5 Da LogP -0.41 TPSA 131.4	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCOCCO`

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GSI6