KpKP13 Protein target profile

Carboxylesterase bioH

Accession: KP13_00681

Gene: AHE42301.1 bioH 3D evidence: Experimental + ColabFold model UniProt A6TF35

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Length 257

Pocket druggability (P2Rank · Experimental) 0.05

Direct ligand evidence 0 59 total records

Functional annotation 0 EC 2 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

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

Main supporting evidence

Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.55. This supports review but is not experimental validation. Structure available Experimental + ColabFold model Review the complete evidence below

Risks to review

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: Hit
Human identity (%): 30.172 Lower values reduce human off-target concern.
Human E-value: 2.3e-06
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: 95.05 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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) 0.05

Structure 6K5E

Pocket Pocket 1

Druggability (FPocket) 0.553

Structure 6K5E

Pocket Pocket 10

ColabFold model

P2Rank 0.152 · Pocket 1

FPocket 0.443 · Pocket 4

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 124 / 4744 genomes with a hit

Prevalence 2.6%

Sequence

Primary amino-acid sequence viewer.

MNDIWWQTIGEGDCHLVLLHGWGLNAQVWDCITPQLASHFTLHLVDLPGYGRSGGFGAMSLEAMAQRVLEQAPPQAVWLGWSLGGLVASQVAIMRPERVQALVTVASSPCFAARDDWPGIKPEVLAGFQQQLSDDFQRTVERFLALQTMGTESARQDARALKQAVLSLPMPSAEALNGGLEILRTVDLRQALVRLPMPFLRLYGRLDGLVPRKIVPLLDDLWPESESILFDKAAHAPFVSHPAAFCEPLLALKTRLG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0009102 The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
GO:0052689 Catalysis of the hydrolysis of a carboxylic ester bond.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
1	255	FunFam	G3DSA:3.40.50.1820:FF:000045	Pimeloyl-[acyl-carrier protein] methyl ester esterase
4	254	SUPERFAMILY	SSF53474	alpha/beta-Hydrolases
4	254	InterPro	IPR029058	Alpha/Beta hydrolase fold
4	254	Hamap	MF_01260	Pimeloyl-[acyl-carrier protein] methyl ester esterase [bioH].
4	254	InterPro	IPR010076	Pimeloyl-[acyl-carrier protein] methyl ester esterase
15	241	Pfam	PF00561	alpha/beta hydrolase fold
15	241	InterPro	IPR000073	Alpha/beta hydrolase fold-1
1	253	Gene3D	G3DSA:3.40.50.1820	alpha/beta hydrolase
1	253	InterPro	IPR029058	Alpha/Beta hydrolase fold
13	250	PANTHER	PTHR43194	HYDROLASE ALPHA/BETA FOLD FAMILY
10	252	NCBIfam	TIGR01738	pimeloyl-ACP methyl ester esterase BioH
10	252	InterPro	IPR010076	Pimeloyl-[acyl-carrier protein] methyl ester esterase

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

0.05

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Surrounding area

Pocket 2 P2Rank #2

0.01

Likely same site as FPocket 2 0.4 Å 8 shared residues 100% of smaller site

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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 #10

0.553

Show in viewer

Surrounding area

Pocket 2 FPocket #2

0.427

Likely same site as P2Rank 2 0.4 Å 8 shared residues 100% of smaller site

Show in viewer

Surrounding area

Pocket 3 FPocket #1

0.21 Unusual size

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Surrounding area

All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 6K5E	X-ray	—	A	—	PDBe RCSB PDBj File	Viewing
ColabFold KP13_00681	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.

59 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 9 records from similar proteins

Structural ligands 9 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

3OH PDB via homolog 90.1 Da · LogP -0.55 · TPSA 57.5 Open detail RCSB PDB

EEE PDB via homolog Detail RCSB PDB

EGC PDB via homolog Detail RCSB PDB

FP6 PDB via homolog Detail RCSB PDB

J6Z 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
3OH RCSB PDB	1M33	P13001	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C(CO)C(=O)O`
EEE RCSB PDB	3HEA	P22862	88.1 Da LogP 0.57 TPSA 26.3	✓ Ro5	✓ Clean	`CCOC(=O)C`
EGC RCSB PDB	5Z95	A0A0M3PNA2	602.8 Da LogP 3.90 TPSA 103.3	1 viol.	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(cc1)OCCOCCOCCOCCOCCOCCOCC…`
FP6 RCSB PDB	7C8L	A0A0M3PNA2	99.1 Da LogP 0.24 TPSA 20.3	✓ Ro5	✓ Clean	`C1CCN(C1)C=O`
J6Z RCSB PDB	3IA2	P22862	137.2 Da LogP 0.33 TPSA 57.2	✓ Ro5	✓ Clean	`CC[C@@H](C)S(=O)(=O)[O-]`
PE3 RCSB PDB	5CBK	A0A0M5I297	634.8 Da LogP -0.81 TPSA 160.5	2 viol.	✓ Clean	`C(COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO)O`
PEO RCSB PDB	3T52	P22862	34.0 Da LogP 0.02 TPSA 40.5	✓ Ro5	✓ Clean	`OO`
TZU RCSB PDB	8DVC	A0A0M5I297	300.3 Da LogP 1.92 TPSA 61.8	✓ Ro5	✓ Clean	`CC1=C[C@@H](OC1=O)OC[C@H]2[C@H]3Cc4ccccc4[C@H]3…`
ZMK RCSB PDB	4ETW	Q83PW0	514.5 Da LogP 0.49 TPSA 188.6	1 viol.	✓ Clean	`CC(C)(COP(=O)(O)O)[C@@H](C(=O)NCCC(=O)NCCSC(=O)…`

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
ZINC2030966 ZINC	1.000	294.4 Da LogP 3.79 TPSA 38.7	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCCO)cc1`
ZINC1532311 ZINC	0.818	250.4 Da LogP 3.77 TPSA 29.5	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCO)cc1`
ZINC35650209 ZINC	0.722	278.4 Da LogP 4.55 TPSA 29.5	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCCCO)cc1`
ZINC1592053 ZINC	0.692	321.5 Da LogP 4.36 TPSA 21.7	✓ Ro5	✓ Clean	`CN(C)CCOCCOc1ccc(C(C)(C)CC(C)(C)C)cc1`
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`
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`
ZINC38917157 ZINC	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
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`
ZINC167273021 ZINC	0.675	308.4 Da LogP 3.88 TPSA 55.8	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCC(=O)O)cc1`
ZINC4353076 ZINC	0.651	352.5 Da LogP 4.42 TPSA 68.3	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCCSC(=N)N)cc1`
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`
ZINC226069334 ZINC	0.628	366.6 Da LogP 3.86 TPSA 38.7	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOC[C@@H](O)C[N+](C)(C)…`
ZINC226069348 ZINC	0.628	366.6 Da LogP 3.86 TPSA 38.7	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOC[C@H](O)C[N+](C)(C)C…`
ZINC3844447 ZINC	0.625	286.3 Da LogP 0.46 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOc1ccc(OCCOCCO)cc1`
ZINC1688152 ZINC	0.609	380.5 Da LogP 3.96 TPSA 55.8	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCC[N+](C)(C)CC(=O)O)c…`
ZINC90741418 ZINC	0.606	242.3 Da LogP 0.45 TPSA 68.2	✓ Ro5	✓ Clean	`OCCOCCOc1ccc(OCCO)cc1`
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`
ZINC1600251 ZINC	0.595	208.3 Da LogP 2.75 TPSA 29.5	✓ Ro5	✓ Clean	`CCC(C)(C)c1ccc(OCCO)cc1`
ZINC1580159 ZINC	0.588	210.3 Da LogP -0.26 TPSA 58.9	✓ Ro5	✓ Clean	`OCCOCCSCCOCCO`
ZINC32011214 ZINC	0.587	363.5 Da LogP 4.13 TPSA 30.9	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCCN2CCOCC2)cc1`
ZINC1648298 ZINC	0.579	206.2 Da LogP -1.17 TPSA 93.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@@H](O)[C@H](O)C(=O)OCC`
ZINC1648299 ZINC	0.579	206.2 Da LogP -1.17 TPSA 93.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@H](O)[C@@H](O)C(=O)OCC`
ZINC1719698 ZINC	0.579	250.2 Da LogP 2.94 TPSA 78.9	✓ Ro5	✓ Clean	`CCOC(=O)P(C(=O)OCC)C(=O)OCC`
ZINC17877781 ZINC	0.579	206.2 Da LogP -1.17 TPSA 93.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@@H](O)[C@@H](O)C(=O)OCC`
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`
ZINC38235275 ZINC	0.579	200.2 Da LogP 1.45 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C(C)=C(/C)C(=O)OCC`
ZINC39200394 ZINC	0.579	200.2 Da LogP 1.45 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C(C)=C(\C)C(=O)OCC`
ZINC79016673 ZINC	0.579	232.3 Da LogP -0.32 TPSA 57.2	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCO`
ZINC83254091 ZINC	0.579	320.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCO`
ZINC96503366 ZINC	0.579	408.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC96503406 ZINC	0.579	276.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCO`
ZINC226069639 ZINC	0.574	365.6 Da LogP 4.15 TPSA 50.7	✓ Ro5	✓ Clean	`CC(C)NC[C@@H](O)COCCOc1ccc(C(C)(C)CC(C)(C)C)cc1`
ZINC226069650 ZINC	0.574	365.6 Da LogP 4.15 TPSA 50.7	✓ Ro5	✓ Clean	`CC(C)NC[C@H](O)COCCOc1ccc(C(C)(C)CC(C)(C)C)cc1`
ZINC16889914 ZINC	0.558	308.5 Da LogP 4.41 TPSA 59.1	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCSC(=N)N)cc1`
ZINC140309458 ZINC	0.556	438.5 Da LogP 3.15 TPSA 88.4	✓ Ro5	✓ Clean	`CC(c1ccc(OCCO)cc1)(c1ccc(OCCO)cc1)c1ccc(OCCO)cc1`
ZINC1531061 ZINC	0.556	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCO`
ZINC1690586 ZINC	0.556	316.4 Da LogP 2.75 TPSA 58.9	✓ Ro5	✓ Clean	`CC(C)(c1ccc(OCCO)cc1)c1ccc(OCCO)cc1`

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 A6TF35

Structure

PDB 6K5E