KpATCC43816 Protein target profile

2,3-diketo-5-methylthio-1-phosphopentane phosphatase

Accession: VK055_1889

Gene: mtnC AIK80495.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 3 reactions UniProt A0A0H3GJW8

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Length 229

Pocket druggability (P2Rank · AlphaFold DB model) 0.786

Metabolic reactions 3

Chokepoint Yes

Direct ligand evidence 0 52 total records

Functional annotation 1 EC 5 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

Main supporting evidence

Metabolic chokepoint Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 89.6% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Review the complete evidence below

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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 (%): 50.0 Lower values reduce human off-target concern.
Human E-value: 8.589999999999998e-41
Gut microbiome similarity: 1.6% 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: 97.16 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) 0.786

Structure A0A0H3GJW8

Pocket Pocket 1

Druggability (FPocket) 0.83

Structure A0A0H3GJW8

Pocket Pocket 11

ColabFold model

P2Rank 0.738 · Pocket 1

FPocket 0.616 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 78 / 4744 genomes with a hit

Prevalence 1.6%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction in Cysteine and methionine metabolism, no isoenzyme backup detected, more central than 89.6% of genes in this genome.

Relative network centrality 89.6% more central than 89.6% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MIRAIVTDIEGTTSDIRFVHNVLFPYARERLAGFVTAQQHAEPVKTILDNLRRETDAPAASTADLITTLFAFMDEDRKSTALKALQGIIWRDGYLNGDFTGHLYPDVLPALEKWKAQGIDLYVYSSGSVAAQKLLFGYSDEGDITHLFTGYFDTLVGAKREVQSYRNIAEHLGHAPGTILFLSDIHQELDAAEAAGLRTVQLVRGDRDPTSHHPQVQRFDDIHPEQIPA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

3.1.3.77

Gene Ontology (GO)

GO:0043874 Catalysis of the reactions:5-methylsulfanyl-2,3-dioxopentyl phosphate + H2O = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0019509 OBSOLETE. The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
GO:0043715 Catalysis of the reaction: 2,3-diketo-5-methylthiopentyl-1-phosphate = H+ + 2-hydroxy 3-keto-5-methylthiopentenyl-1-phosphate. 2,3-diketo-5-methylthiopentyl-1-phosphate is also known as DK-MTP-1-P, and 2-hydroxy 3-keto-5-methylthiopentenyl-1-phosphate as HK-MTPenyl-1-P.
GO:0043716 Catalysis of the reaction: 2-hydroxy-5-methylsulfanyl-3-oxopent-1-enyl phosphate + H2O = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records

Show feature table

Start	End	DB	Term	Name
2	196	Pfam	PF00702	haloacid dehalogenase-like hydrolase
205	229	MobiDBLite	mobidb-lite	consensus disorder prediction
2	13	PRINTS	PR00413	Haloacid dehalogenase/epoxide hydrolase family signature
2	13	InterPro	IPR006439	HAD hydrolase, subfamily IA
114	127	PRINTS	PR00413	Haloacid dehalogenase/epoxide hydrolase family signature
114	127	InterPro	IPR006439	HAD hydrolase, subfamily IA
164	184	PRINTS	PR00413	Haloacid dehalogenase/epoxide hydrolase family signature
164	184	InterPro	IPR006439	HAD hydrolase, subfamily IA
191	204	PRINTS	PR00413	Haloacid dehalogenase/epoxide hydrolase family signature
191	204	InterPro	IPR006439	HAD hydrolase, subfamily IA
16	99	Gene3D	G3DSA:1.10.720.60	-
97	212	FunFam	G3DSA:3.40.50.1000:FF:000079	Enolase-phosphatase E1
1	222	SUPERFAMILY	SSF56784	HAD-like
1	222	InterPro	IPR036412	HAD-like superfamily
116	196	NCBIfam	TIGR01549	HAD-IA family hydrolase
116	196	InterPro	IPR006439	HAD hydrolase, subfamily IA
205	220	MobiDBLite	mobidb-lite	consensus disorder prediction
1	223	SFLD	SFLDS00003	Haloacid Dehalogenase
1	222	Hamap	MF_01681	Enolase-phosphatase E1 [mtnC].
1	222	InterPro	IPR023943	Enolase-phosphatase E1
1	223	SFLD	SFLDF00044	enolase-phosphatase
1	223	InterPro	IPR023943	Enolase-phosphatase E1
6	211	Gene3D	G3DSA:3.40.50.1000	-
6	211	InterPro	IPR023214	HAD superfamily
2	222	NCBIfam	TIGR01691	acireductone synthase
2	222	InterPro	IPR023943	Enolase-phosphatase E1
2	221	PANTHER	PTHR20371	ENOLASE-PHOSPHATASE E1
4	204	CDD	cd01629	HAD_EP
4	204	InterPro	IPR023943	Enolase-phosphatase E1

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

0.786

Likely same site as FPocket 11 1.8 Å 17 shared residues 77% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.05

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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 #11

0.83 Unusual size

Likely same site as P2Rank 1 1.8 Å 17 shared residues 77% of smaller site

Show in viewer

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_A0A0H3GJW8	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_1889	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.

52 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 2 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

HPO PDB via homolog 194.2 Da · LogP 1.31 · TPSA 74.6 Open detail RCSB PDB

PE4 PDB via homolog Detail RCSB PDB

ZINC5650743 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC6403917 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC12501520 ZINC proposed compound · Tanimoto 0.688 Detail ZINC

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
HPO RCSB PDB	1YNS	Q9UHY7	194.2 Da LogP 1.31 TPSA 74.6	✓ Ro5	✓ Clean	`CCCCCC(=O)CP(=O)(O)O`
PE4 RCSB PDB	2G80	P32626	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`

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
ZINC5650743 ZINC	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917 ZINC	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC12501520 ZINC	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716 ZINC	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769 ZINC	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548 ZINC	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829 ZINC	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830 ZINC	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5859031 ZINC	0.688	294.4 Da LogP 1.13 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCC`
ZINC2539249 ZINC	0.621	222.2 Da LogP 2.62 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCCC(=O)CP(=O)(OC)OC`
ZINC1644613 ZINC	0.619	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC1580161 ZINC	0.600	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118 ZINC	0.600	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257 ZINC	0.600	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654 ZINC	0.600	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059 ZINC	0.600	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44963221 ZINC	0.600	250.3 Da LogP 3.40 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CP(=O)(OC)OC`
ZINC5210101 ZINC	0.600	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860 ZINC	0.600	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC91695991 ZINC	0.600	250.3 Da LogP 3.40 TPSA 52.6	✓ Ro5	✓ Clean	`CCCCCC(=O)CP(=O)(OCC)OCC`
ZINC2555269 ZINC	0.591	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC4974293 ZINC	0.579	280.4 Da LogP 1.08 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCOCCOCCOCC`
ZINC100014200 ZINC	0.565	494.7 Da LogP 4.02 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC100070166 ZINC	0.565	290.4 Da LogP 3.17 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCO`
ZINC100310628 ZINC	0.565	478.7 Da LogP 4.78 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC100365196 ZINC	0.565	302.5 Da LogP 4.71 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCO`
ZINC101772322 ZINC	0.565	434.7 Da LogP 4.76 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC103600921 ZINC	0.565	466.7 Da LogP 3.24 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC14880431 ZINC	0.565	378.6 Da LogP 3.20 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC14881140 ZINC	0.565	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
ZINC16051619 ZINC	0.565	350.5 Da LogP 2.42 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCOCCO`
ZINC2584424 ZINC	0.565	218.3 Da LogP 2.37 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCO`
ZINC4521877 ZINC	0.565	234.3 Da LogP 1.61 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCO`
ZINC5273610 ZINC	0.565	322.4 Da LogP 1.64 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCOCCOCCO`
ZINC58538366 ZINC	0.565	392.6 Da LogP 3.59 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC58631420 ZINC	0.565	422.6 Da LogP 3.22 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC59441819 ZINC	0.565	318.5 Da LogP 3.95 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCO`
ZINC59622400 ZINC	0.565	274.4 Da LogP 3.93 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCO`
ZINC71788551 ZINC	0.565	334.5 Da LogP 3.19 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCO`
ZINC71788564 ZINC	0.565	262.4 Da LogP 2.39 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCO`
ZINC71788567 ZINC	0.565	406.6 Da LogP 3.98 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC8214594 ZINC	0.565	362.6 Da LogP 3.97 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC88260008 ZINC	0.565	390.6 Da LogP 4.75 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC95784968 ZINC	0.565	450.7 Da LogP 4.00 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC95863931 ZINC	0.565	464.7 Da LogP 4.39 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC1606037 ZINC	0.560	212.4 Da LogP 4.89 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCC`
ZINC116078620 ZINC	0.538	236.3 Da LogP -0.41 TPSA 74.2	✓ Ro5	✓ Clean	`CCOC(=O)COCCOCCOCCO`
ZINC116852907 ZINC	0.538	240.4 Da LogP 4.46 TPSA 34.1	✓ Ro5	✓ Clean	`CCCCCCC(=O)CC(=O)CCCCCC`
ZINC1606038 ZINC	0.538	212.4 Da LogP 4.89 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CC`
ZINC83253955 ZINC	0.538	206.2 Da LogP -0.03 TPSA 65.0	✓ Ro5	✓ Clean	`CCOC(=O)CCOCCOCCO`

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 A0A0H3GJW8

Pathways

KEGG R07395 BioCyc 3.1.3.77-RXN KEGG R07393 BioCyc R82-RXN KEGG R07394 BioCyc R83-RXN