KpKP13 Protein target profile

S-formylglutathione hydrolase

Accession: KP13_05055

Gene: AHE43572.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GST9

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Length 277

Pocket druggability (P2Rank · AlphaFold DB model) 0.355

Direct ligand evidence 0 56 total records

Functional annotation 1 EC 4 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

Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 2 structural and 4 bioactivity records.

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 (%): 53.571 Lower values reduce human off-target concern.
Human E-value: 2.27e-92
Gut microbiome similarity: 3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 51.812 Higher values support similarity to known essential genes.
DEG E-value: 7.84e-102 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 98.07 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) 0.355

Structure A0A0H3GST9

Pocket Pocket 1

Druggability (FPocket) 0.324

Structure A0A0H3GST9

Pocket Pocket 3

ColabFold model

P2Rank 0.588 · Pocket 1

FPocket 0.387 · Pocket 3

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 166 / 4744 genomes with a hit

Prevalence 3.5%

Sequence

Primary amino-acid sequence viewer.

MELLEEHRCFDGQQQRWRHHSPVLNCAMTFSIFLPPERETPPPVLYWLSGLTCNDENFTTKAGAQRIAAELGIALVMPDTSPRGDEAANDDGYDLGQGAGFYLNATEAPWAAHYRMYDYLRDELPALIRSEFSVGECCAVSGHSMGGHGALIMALKNPGRYASVSAFAPIVNPSQVPWGKKAFTAYLGADESAWHSWDSCALMQASRPEDAVPTLIDQGDNDPFLAGQLQPAVLAEVARQKAWPLTLRIQPGYDHSYYFIASFIEDHLRFHAQHLFG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization: Unknown

Enzyme Commission (EC)

3.1.2.12

Gene Ontology (GO)

GO:0018738 Catalysis of the reaction: S-formylglutathione + H2O = formate + glutathione + H+.
GO:0046294 The chemical reactions and pathways resulting in the breakdown of formaldehyde (methanal, H2C=O), the simplest aldehyde.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
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.

11 records

Show feature table

Start	End	DB	Term	Name
1	276	Gene3D	G3DSA:3.40.50.1820	alpha/beta hydrolase
1	276	InterPro	IPR029058	Alpha/Beta hydrolase fold
1	275	SUPERFAMILY	SSF53474	alpha/beta-Hydrolases
1	275	InterPro	IPR029058	Alpha/Beta hydrolase fold
3	275	PANTHER	PTHR10061	S-FORMYLGLUTATHIONE HYDROLASE
3	275	InterPro	IPR014186	S-formylglutathione hydrolase
1	276	FunFam	G3DSA:3.40.50.1820:FF:000002	S-formylglutathione hydrolase
2	275	NCBIfam	TIGR02821	S-formylglutathione hydrolase
2	275	InterPro	IPR014186	S-formylglutathione hydrolase
21	270	Pfam	PF00756	Putative esterase
21	270	InterPro	IPR000801	Esterase-like

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

0.355

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Surrounding area

Pocket 2 P2Rank #2

0.01

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Surrounding area

Pocket 3 P2Rank #3

0.002

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Surrounding area

Pocket 4 P2Rank #4

0.001

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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

0.324

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Surrounding area

Residue sets

UniProt: Active site:144-144 Charge relay system

UniProt: Active site:222-222 Charge relay system

UniProt: Active site:255-255 Charge relay system

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_A0A0H3GST9	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_05055	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.

56 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records

Transferred evidence 6 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 4 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

6WG PDB via homolog 189.3 Da · LogP 2.37 · TPSA 20.3 Open detail RCSB PDB

HE4 PDB via homolog Detail RCSB PDB

CHEMBL4635246 ChEMBL via homolog · pchembl 9.10 (~0.8 nM) Detail ChEMBL

CHEMBL157404 ChEMBL via homolog · pchembl 7.89 (~12.9 nM) Detail ChEMBL

DWT ChEMBL via homolog · pchembl 6.93 (~117.5 nM) Detail ChEMBL

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
6WG RCSB PDB	6VHD	Q2FUY3	189.3 Da LogP 2.37 TPSA 20.3	✓ Ro5	✓ Clean	`c1ccc(cc1)[C@H]2CCCCN2C=O`
HE4 RCSB PDB	6WCX	Q2FUY3	116.2 Da LogP 1.95 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCO`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL4635246 ChEMBL	P10768	9.10 ~0.8 nM	349.8 Da LogP 4.80 TPSA 48.7	✓ Ro5	Alert	`Oc1ccc(Cl)cc1C1=NN(c2ccccn2)C(c2ccccc2)C1`
CHEMBL157404 ChEMBL	Q9GJT2	7.89 ~12.9 nM	762.2 Da LogP 1.79 TPSA 223.4	2 viol.	✓ Clean	`COC(=O)/C(OC(C)=O)=C(\NC(=O)[C@@H]1CCCN1C(=O)[C…`
DWT ChEMBL	P10768	6.93 ~117.5 nM	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
CHEMBL160446 ChEMBL	Q9GJT2	6.89 ~128.8 nM	554.6 Da LogP -0.34 TPSA 186.5	1 viol.	✓ Clean	`COC(=O)CCC(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N1C…`

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
ZINC1644076 ZINC	1.000	214.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCO`
ZINC1680803 ZINC	1.000	200.4 Da LogP 4.29 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCO`
ZINC72221860 ZINC	0.706	207.2 Da LogP 2.51 TPSA 20.3	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1ccc(F)cc1`
ZINC72221861 ZINC	0.706	207.2 Da LogP 2.51 TPSA 20.3	✓ Ro5	✓ Clean	`O=CN1CCCC[C@@H]1c1ccc(F)cc1`
ZINC2149802 ZINC	0.684	210.4 Da LogP 3.90 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCC#CCCCCCCO`
ZINC2555300 ZINC	0.684	238.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCC#CCCCCCCCCO`
ZINC2579260 ZINC	0.684	238.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCC#CCCCCCCO`
ZINC59724910 ZINC	0.684	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCCO`
ZINC59724924 ZINC	0.684	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCO`
ZINC59724927 ZINC	0.684	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCO`
ZINC95831576 ZINC	0.684	230.4 Da LogP 3.92 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCCCO`
ZINC72221525 ZINC	0.649	219.3 Da LogP 2.38 TPSA 29.5	✓ Ro5	✓ Clean	`COc1ccc([C@@H]2CCCCN2C=O)cc1`
ZINC72221526 ZINC	0.649	219.3 Da LogP 2.38 TPSA 29.5	✓ Ro5	✓ Clean	`COc1ccc([C@H]2CCCCN2C=O)cc1`
ZINC15721440 ZINC	0.636	470.5 Da LogP -0.83 TPSA 171.2	✓ Ro5	✓ Clean	`COC(=O)CCC(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N1C…`
ZINC2080120662 ZINC	0.632	234.3 Da LogP 2.28 TPSA 63.5	✓ Ro5	✓ Clean	`O=CN1CCCC[C@@H]1c1ccc([N+](=O)[O-])cc1`
ZINC2080120663 ZINC	0.632	234.3 Da LogP 2.28 TPSA 63.5	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1ccc([N+](=O)[O-])cc1`
ZINC100244447 ZINC	0.619	276.5 Da LogP 4.04 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@@](=O)CCCCCCCO`
ZINC100244449 ZINC	0.619	276.5 Da LogP 4.04 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCCCCCCO`
ZINC98008412 ZINC	0.619	250.4 Da LogP 2.53 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCCCO`
ZINC98008413 ZINC	0.619	234.4 Da LogP 2.87 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@@](=O)CCCCO`
ZINC98008414 ZINC	0.619	234.4 Da LogP 2.87 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCCCO`
ZINC14771652 ZINC	0.615	216.4 Da LogP 3.26 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCO`
ZINC15269439 ZINC	0.615	272.5 Da LogP 4.82 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCCCO`
ZINC1574339 ZINC	0.615	202.3 Da LogP 2.87 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCO`
ZINC4202510 ZINC	0.615	230.4 Da LogP 3.65 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCO`
ZINC4521552 ZINC	0.615	258.4 Da LogP 4.43 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCCO`
ZINC4600152 ZINC	0.615	244.4 Da LogP 4.04 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCO`
ZINC72217633 ZINC	0.605	298.4 Da LogP 3.92 TPSA 33.2	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1ccc(Sc2ccccc2)nc1`
ZINC72217634 ZINC	0.605	298.4 Da LogP 3.92 TPSA 33.2	✓ Ro5	✓ Clean	`O=CN1CCCC[C@@H]1c1ccc(Sc2ccccc2)nc1`
ZINC100245871 ZINC	0.600	232.4 Da LogP 4.24 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCSCCCO`
ZINC1682375 ZINC	0.600	215.4 Da LogP 3.05 TPSA 23.5	✓ Ro5	✓ Clean	`CCCCN(CCCC)CCCCCO`
ZINC2009358 ZINC	0.600	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCCCO`
ZINC2555306 ZINC	0.600	238.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCC#CCCCCCCCCCCO`
ZINC2555345 ZINC	0.600	210.4 Da LogP 3.90 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCC#CCCCCCCCCO`
ZINC4409966 ZINC	0.600	257.5 Da LogP 4.22 TPSA 23.5	✓ Ro5	✓ Clean	`CCCCN(CCCC)CCCCCCCCO`
ZINC4409972 ZINC	0.600	271.5 Da LogP 4.61 TPSA 23.5	✓ Ro5	✓ Clean	`CCCCN(CCCC)CCCCCCCCCO`
ZINC4528894 ZINC	0.600	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCCO`
ZINC545509 ZINC	0.600	314.8 Da LogP 3.74 TPSA 52.9	✓ Ro5	Alert	`CC(=O)N1N=C(c2cc(Cl)ccc2O)C[C@@H]1c1ccccc1`
ZINC545510 ZINC	0.600	314.8 Da LogP 3.74 TPSA 52.9	✓ Ro5	Alert	`CC(=O)N1N=C(c2cc(Cl)ccc2O)C[C@H]1c1ccccc1`
ZINC59545536 ZINC	0.600	258.4 Da LogP 4.70 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCCO`
ZINC72219597 ZINC	0.595	240.3 Da LogP 2.92 TPSA 33.2	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1cnc2ccccc2c1`
ZINC72219598 ZINC	0.595	240.3 Da LogP 2.92 TPSA 33.2	✓ Ro5	✓ Clean	`O=CN1CCCC[C@@H]1c1cnc2ccccc2c1`
ZINC104156515 ZINC	0.591	283.5 Da LogP 4.80 TPSA 42.2	✓ Ro5	✓ Clean	`CCCCCCCC[C@H]1N[C@H]1CCCCCCCCO`
ZINC104156519 ZINC	0.591	283.5 Da LogP 4.80 TPSA 42.2	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H]1N[C@H]1CCCCCCCCO`
ZINC104156523 ZINC	0.591	283.5 Da LogP 4.80 TPSA 42.2	✓ Ro5	✓ Clean	`CCCCCCCC[C@H]1N[C@@H]1CCCCCCCCO`
ZINC104156528 ZINC	0.591	283.5 Da LogP 4.80 TPSA 42.2	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H]1N[C@@H]1CCCCCCCCO`
ZINC72212171 ZINC	0.591	282.3 Da LogP 3.56 TPSA 42.4	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1ccc(Oc2ccccc2)nc1`
ZINC72212172 ZINC	0.591	282.3 Da LogP 3.56 TPSA 42.4	✓ Ro5	✓ Clean	`O=CN1CCCC[C@@H]1c1ccc(Oc2ccccc2)nc1`
ZINC72214110 ZINC	0.591	281.4 Da LogP 3.51 TPSA 45.2	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1ccc(Nc2ccccc2)nc1`
ZINC72214111 ZINC	0.591	281.4 Da LogP 3.51 TPSA 45.2	✓ Ro5	✓ Clean	`O=CN1CCCC[C@@H]1c1ccc(Nc2ccccc2)nc1`

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 A0A0H3GST9

Chemistry

ChEMBL CHEMBL4635246 ChEMBL CHEMBL157404 ChEMBL DWT ChEMBL CHEMBL160446