Protein profile

KP13_05055

S-formylglutathione hydrolase

Genome: KpKP13

Gene: AHE43572.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GST9

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Amino acids 277

Annotations 5

Features 11

PDB binders 2

Druggability 0.324

Overview

Basic information about this protein and its source genome.

Accession: KP13_05055
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43572.1
Status: annotated
Amino acids: 277
Structure source: AlphaFold + ColabFold

3.1.2.12

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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 53.571
Human E-value: 2.27e-92
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 51.812
DEG E-value: 7.84e-102
Localization: Unknown
ColabFold pLDDT: 98.07

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.324

Structure A0A0H3GST9

Pocket Pocket 3

P2Rank 0.355

Structure A0A0H3GST9

Pocket Pocket 1

ColabFold model

FPocket 0.387 · Pocket 3

P2Rank 0.588 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 166 / 4744 genomes with a hit

Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GST9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05055	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
3				0.324

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	4.6	0.198
2	0.62	0.0
3	0.59	0.0

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
3				0.387
9				0.291

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				7.71	0.408

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

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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	6VHD	Q2FUY3	189.3 Da LogP 2.37 TPSA 20.3	✓ Ro5	✓ Clean	`c1ccc(cc1)[C@H]2CCCCN2C=O`
HE4	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	P10768	9.10	349.8 Da LogP 4.80 TPSA 48.7	✓ Ro5	Alert	`Oc1ccc(Cl)cc1C1=NN(c2ccccn2)C(c2ccccc2)C1`
CHEMBL157404	Q9GJT2	7.89	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	P10768	6.93	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
CHEMBL160446	Q9GJT2	6.89	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	1.000	214.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCO`
ZINC1680803	1.000	200.4 Da LogP 4.29 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCO`
ZINC72221860	0.706	207.2 Da LogP 2.51 TPSA 20.3	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1ccc(F)cc1`
ZINC72221861	0.706	207.2 Da LogP 2.51 TPSA 20.3	✓ Ro5	✓ Clean	`O=CN1CCCC[C@@H]1c1ccc(F)cc1`
ZINC2149802	0.684	210.4 Da LogP 3.90 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCC#CCCCCCCO`
ZINC2555300	0.684	238.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCC#CCCCCCCCCO`
ZINC2579260	0.684	238.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCC#CCCCCCCO`
ZINC59724910	0.684	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCCO`
ZINC59724924	0.684	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCO`
ZINC59724927	0.684	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCO`
ZINC95831576	0.684	230.4 Da LogP 3.92 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCCCO`
ZINC72221525	0.649	219.3 Da LogP 2.38 TPSA 29.5	✓ Ro5	✓ Clean	`COc1ccc([C@@H]2CCCCN2C=O)cc1`
ZINC72221526	0.649	219.3 Da LogP 2.38 TPSA 29.5	✓ Ro5	✓ Clean	`COc1ccc([C@H]2CCCCN2C=O)cc1`
ZINC15721440	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	0.632	234.3 Da LogP 2.28 TPSA 63.5	✓ Ro5	✓ Clean	`O=CN1CCCC[C@@H]1c1ccc([N+](=O)[O-])cc1`
ZINC2080120663	0.632	234.3 Da LogP 2.28 TPSA 63.5	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1ccc([N+](=O)[O-])cc1`
ZINC100244447	0.619	276.5 Da LogP 4.04 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@@](=O)CCCCCCCO`
ZINC100244449	0.619	276.5 Da LogP 4.04 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCCCCCCO`
ZINC98008412	0.619	250.4 Da LogP 2.53 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCS(=O)(=O)CCCCO`
ZINC98008413	0.619	234.4 Da LogP 2.87 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@@](=O)CCCCO`
ZINC98008414	0.619	234.4 Da LogP 2.87 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCCCO`
ZINC14771652	0.615	216.4 Da LogP 3.26 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCO`
ZINC15269439	0.615	272.5 Da LogP 4.82 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCCCO`
ZINC1574339	0.615	202.3 Da LogP 2.87 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCO`
ZINC4202510	0.615	230.4 Da LogP 3.65 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCO`
ZINC4521552	0.615	258.4 Da LogP 4.43 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCCO`
ZINC4600152	0.615	244.4 Da LogP 4.04 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCO`
ZINC72217633	0.605	298.4 Da LogP 3.92 TPSA 33.2	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1ccc(Sc2ccccc2)nc1`
ZINC72217634	0.605	298.4 Da LogP 3.92 TPSA 33.2	✓ Ro5	✓ Clean	`O=CN1CCCC[C@@H]1c1ccc(Sc2ccccc2)nc1`
ZINC100245871	0.600	232.4 Da LogP 4.24 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCCCCCCCSCCCO`
ZINC1682375	0.600	215.4 Da LogP 3.05 TPSA 23.5	✓ Ro5	✓ Clean	`CCCCN(CCCC)CCCCCO`
ZINC2009358	0.600	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCCCO`
ZINC2555306	0.600	238.4 Da LogP 4.68 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCC#CCCCCCCCCCCO`
ZINC2555345	0.600	210.4 Da LogP 3.90 TPSA 20.2	✓ Ro5	✓ Clean	`CCCCC#CCCCCCCCCO`
ZINC4409966	0.600	257.5 Da LogP 4.22 TPSA 23.5	✓ Ro5	✓ Clean	`CCCCN(CCCC)CCCCCCCCO`
ZINC4409972	0.600	271.5 Da LogP 4.61 TPSA 23.5	✓ Ro5	✓ Clean	`CCCCN(CCCC)CCCCCCCCCO`
ZINC4528894	0.600	212.4 Da LogP 4.46 TPSA 20.2	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCCO`
ZINC545509	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	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	0.600	258.4 Da LogP 4.70 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCCO`
ZINC72219597	0.595	240.3 Da LogP 2.92 TPSA 33.2	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1cnc2ccccc2c1`
ZINC72219598	0.595	240.3 Da LogP 2.92 TPSA 33.2	✓ Ro5	✓ Clean	`O=CN1CCCC[C@@H]1c1cnc2ccccc2c1`
ZINC104156515	0.591	283.5 Da LogP 4.80 TPSA 42.2	✓ Ro5	✓ Clean	`CCCCCCCC[C@H]1N[C@H]1CCCCCCCCO`
ZINC104156519	0.591	283.5 Da LogP 4.80 TPSA 42.2	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H]1N[C@H]1CCCCCCCCO`
ZINC104156523	0.591	283.5 Da LogP 4.80 TPSA 42.2	✓ Ro5	✓ Clean	`CCCCCCCC[C@H]1N[C@@H]1CCCCCCCCO`
ZINC104156528	0.591	283.5 Da LogP 4.80 TPSA 42.2	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H]1N[C@@H]1CCCCCCCCO`
ZINC72212171	0.591	282.3 Da LogP 3.56 TPSA 42.4	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1ccc(Oc2ccccc2)nc1`
ZINC72212172	0.591	282.3 Da LogP 3.56 TPSA 42.4	✓ Ro5	✓ Clean	`O=CN1CCCC[C@@H]1c1ccc(Oc2ccccc2)nc1`
ZINC72214110	0.591	281.4 Da LogP 3.51 TPSA 45.2	✓ Ro5	✓ Clean	`O=CN1CCCC[C@H]1c1ccc(Nc2ccccc2)nc1`
ZINC72214111	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.