KpATCC43816 Protein target profile

o-succinylbenzoate synthase

Accession: VK055_4856

Gene: menC AIK83383.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3H0Z7

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Length 321

Pocket druggability (P2Rank · AlphaFold DB model) 0.632

Metabolic reactions 1

Chokepoint Yes

Direct ligand evidence 0 53 total records

Functional annotation 1 EC 4 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 94.4% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. 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: 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 (%): 29.964 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 95.98 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) 0.632

Structure A0A0H3H0Z7

Pocket Pocket 1

Druggability (FPocket) 0.619

Structure A0A0H3H0Z7

Pocket Pocket 4

ColabFold model

P2Rank 0.691 · Pocket 1

FPocket 0.191 · Pocket 16

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 125 / 4744 genomes with a hit

Prevalence 2.6%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction in Ubiquinone and other terpenoid-quinone biosynthesis, no isoenzyme backup detected, more central than 94.4% of genes in this genome, no human homolog detected.

Relative network centrality 94.4% more central than 94.4% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MRVSQVYRWQIPMDAGVVLRERRLKTRDGLFIRLQEGEREGWGEISPLPGFSVETLEEAQMALLAWAQAWRDGAEPPLPTQPSVAFGISCAQAELSGGLPQAADYRAAPLCSGDPDELFARLAAMPGEKVAKVKVGLWEAVRDGMVVNLLLEAIPDLQLRLDANRAWTPLKAQQFAKYVNPAYRQRIAFLEEPCKTREDSRAFSRETGIAIAWDESLREADFRFVAEPGVRAVVIKPTLTGSLQKVQQQVAAAHALGLSVVISSSIESSLGLTQLARIAAWLTPQTIPGLDTLSLMGAQLVRPWPESALPVLNIDALEPLL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization: CytoplasmicMembrane

Enzyme Commission (EC)

4.2.1.113

Gene Ontology (GO)

GO:0000287 Binding to a magnesium (Mg) ion.
GO:0009234 The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
GO:0043748 Catalysis of the reaction: 2-succinylbenzoate + H2O = 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
5	311	SFLD	SFLDG00180	muconate cycloisomerase
4	321	Hamap	MF_00470	o-succinylbenzoate synthase [menC].
4	321	InterPro	IPR010196	o-Succinylbenzoate synthase, MenC type1
107	307	SUPERFAMILY	SSF51604	Enolase C-terminal domain-like
107	307	InterPro	IPR036849	Enolase-like, C-terminal domain superfamily
5	311	SFLD	SFLDF00009	o-succinylbenzoate synthase
5	314	PANTHER	PTHR48073	O-SUCCINYLBENZOATE SYNTHASE-RELATED
1	311	Gene3D	G3DSA:3.30.390.10	-
1	311	InterPro	IPR029017	Enolase-like, N-terminal
122	282	Pfam	PF13378	Enolase C-terminal domain-like
122	282	InterPro	IPR029065	Enolase C-terminal domain-like
5	292	CDD	cd03320	OSBS
115	210	SMART	SM00922	MR_MLE_2
115	210	InterPro	IPR013342	Mandelate racemase/muconate lactonizing enzyme, C-terminal
1	99	SUPERFAMILY	SSF54826	Enolase N-terminal domain-like
1	99	InterPro	IPR029017	Enolase-like, N-terminal
7	307	NCBIfam	TIGR01927	o-succinylbenzoate synthase
98	295	FunFam	G3DSA:3.20.20.120:FF:000006	o-succinylbenzoate synthase
98	295	Gene3D	G3DSA:3.20.20.120	-
98	295	InterPro	IPR036849	Enolase-like, C-terminal domain 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

0.632

Likely same site as FPocket 4 3.9 Å 20 shared residues 91% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.06

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Surrounding area

Pocket 3 P2Rank #3

0.037

Likely same site as FPocket 2 1.7 Å 11 shared residues 100% of smaller site

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Surrounding area

Pocket 4 P2Rank #4

0.019

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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 #4

0.619 Unusual size

Likely same site as P2Rank 1 3.9 Å 20 shared residues 91% of smaller site

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Surrounding area

Pocket 2 FPocket #2

0.545

Likely same site as P2Rank 3 1.7 Å 11 shared residues 100% of smaller site

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Surrounding area

Residue sets

UniProt: Active site:134-134 Proton donor

UniProt: Active site:236-236 Proton acceptor

UniProt: Binding site:162-162

UniProt: Binding site:191-191

UniProt: Binding site:214-214

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.691

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Surrounding area

Pocket 2 P2Rank #2

0.033

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Surrounding area

Pocket 3 P2Rank #3

0.018

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Surrounding area

Residue sets

UniProt: Active site:134-134 Proton donor

UniProt: Active site:236-236 Proton acceptor

UniProt: Binding site:162-162

UniProt: Binding site:191-191

UniProt: Binding site:214-214

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_A0A0H3H0Z7	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_4856	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.

53 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

164 PDB via homolog 240.2 Da · LogP -0.02 · TPSA 111.9 Open detail RCSB PDB

OSB PDB via homolog Detail RCSB PDB

SIN PDB via homolog Detail RCSB PDB

ZINC1604722 ZINC proposed compound · Tanimoto 0.870 Detail ZINC

ZINC2518017 ZINC proposed compound · Tanimoto 0.679 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
164 RCSB PDB	1R6W	P29208	240.2 Da LogP -0.02 TPSA 111.9	✓ Ro5	✓ Clean	`C1=C[C@H]([C@@H](C(=C1)C(=O)CCC(=O)O)C(=O)O)O`
OSB RCSB PDB	1FHV	P29208	222.2 Da LogP 1.43 TPSA 91.7	✓ Ro5	✓ Clean	`c1ccc(c(c1)C(=O)CCC(=O)O)C(=O)O`
SIN RCSB PDB	3GC2	P58486	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)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
ZINC1604722 ZINC	0.870	326.3 Da LogP 2.93 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)CCC(=O)c1ccccc1C(=O)O`
ZINC2518017 ZINC	0.679	212.6 Da LogP 2.39 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1ccccc1Cl`
ZINC343704 ZINC	0.667	208.2 Da LogP 1.04 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CC(=O)c1ccccc1C(=O)O`
ZINC2567379 ZINC	0.655	257.1 Da LogP 2.50 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1ccccc1Br`
ZINC2579878 ZINC	0.655	304.1 Da LogP 2.34 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1ccccc1I`
ZINC14619964 ZINC	0.633	206.2 Da LogP 2.76 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)c1ccccc1C(=O)O`
ZINC236510 ZINC	0.633	228.2 Da LogP 2.89 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1cccc2ccccc12`
ZINC52201682 ZINC	0.633	206.2 Da LogP 2.30 TPSA 54.4	✓ Ro5	✓ Clean	`CCc1ccccc1C(=O)CCC(=O)O`
ZINC1529497 ZINC	0.615	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045 ZINC	0.615	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115 ZINC	0.615	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020 ZINC	0.615	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440 ZINC	0.615	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298 ZINC	0.615	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062 ZINC	0.615	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC1594157 ZINC	0.586	240.3 Da LogP 2.81 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)Cc1ccccc1`
ZINC518924 ZINC	0.586	284.3 Da LogP 2.51 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1CC(=O)c1ccccc1C(=O)O`
ZINC1572706 ZINC	0.563	260.2 Da LogP -1.05 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)NCCNC(=O)CCC(=O)O`
ZINC77311440 ZINC	0.563	238.2 Da LogP 1.02 TPSA 100.9	✓ Ro5	✓ Clean	`O=C(O)CCOC(=O)c1ccccc1C(=O)O`
ZINC2579968 ZINC	0.559	222.2 Da LogP 2.13 TPSA 63.6	✓ Ro5	✓ Clean	`CCOc1ccccc1C(=O)CCC(=O)O`
ZINC82289160 ZINC	0.559	221.2 Da LogP 1.30 TPSA 83.5	✓ Ro5	✓ Clean	`O=CNc1ccccc1C(=O)CCC(=O)O`
ZINC1671412 ZINC	0.533	234.3 Da LogP 2.08 TPSA 71.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)CCC(=O)c1ccccc1`
ZINC1703342 ZINC	0.533	202.2 Da LogP 1.07 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)CCCC(=O)O`
ZINC1728397 ZINC	0.533	233.2 Da LogP -0.29 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)CCN(CCC(=O)O)CCC(=O)O`
ZINC2508031 ZINC	0.533	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)CCCCC(=O)O`
ZINC2517013 ZINC	0.533	250.2 Da LogP 0.89 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)CCP(CCC(=O)O)CCC(=O)O`
ZINC9095223 ZINC	0.533	356.3 Da LogP 1.24 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)NCCNC(=O)c1ccccc1C(=O)O`
ZINC13356583 ZINC	0.531	207.2 Da LogP 1.71 TPSA 80.4	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)CCCC(=O)O`
ZINC2378634 ZINC	0.531	206.2 Da LogP 2.43 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccccc1C(=O)CCCC(=O)O`
ZINC2378735 ZINC	0.531	210.2 Da LogP 2.26 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)c1ccccc1F`
ZINC2518019 ZINC	0.531	240.7 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)c1ccccc1Cl`
ZINC2567373 ZINC	0.531	271.1 Da LogP 2.89 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)c1ccccc1Br`
ZINC2579879 ZINC	0.531	318.1 Da LogP 2.73 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)c1ccccc1I`
ZINC26895996 ZINC	0.531	208.2 Da LogP 1.79 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCc1ccccc1C(=O)O`
ZINC1697439 ZINC	0.529	219.5 Da LogP 1.79 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)C(Cl)(Cl)Cl`
ZINC2024475 ZINC	0.529	251.2 Da LogP 0.98 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)CCCNC(=O)c1ccccc1C(=O)O`
ZINC35465466 ZINC	0.529	244.3 Da LogP 2.24 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC(=O)CCC(=O)O`
ZINC39208104 ZINC	0.529	262.2 Da LogP -0.20 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)OCCOC(=O)CCC(=O)O`
ZINC15080701 ZINC	0.517	222.2 Da LogP 1.43 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1ccc(C(=O)O)cc1`
ZINC1427 ZINC	0.516	254.3 Da LogP 3.40 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1ccc(-c2ccccc2)cc1`
ZINC167997 ZINC	0.515	209.2 Da LogP 1.27 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)CCNc1ccccc1C(=O)O`
ZINC1721300 ZINC	0.515	270.3 Da LogP 3.07 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCc1ccccc1-c1ccccc1C(=O)O`
ZINC2378635 ZINC	0.515	220.3 Da LogP 2.82 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccccc1C(=O)CCCCC(=O)O`
ZINC2378696 ZINC	0.515	242.3 Da LogP 3.28 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)c1cccc2ccccc12`
ZINC2378736 ZINC	0.515	224.2 Da LogP 2.65 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)c1ccccc1F`
ZINC2518020 ZINC	0.515	254.7 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)c1ccccc1Cl`
ZINC2518021 ZINC	0.515	268.7 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)c1ccccc1Cl`
ZINC2567374 ZINC	0.515	285.1 Da LogP 3.28 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)c1ccccc1Br`
ZINC2579880 ZINC	0.515	332.1 Da LogP 3.12 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)c1ccccc1I`
ZINC95634282 ZINC	0.515	220.3 Da LogP 2.69 TPSA 54.4	✓ Ro5	✓ Clean	`CCc1ccccc1C(=O)CCCC(=O)O`

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 A0A0H3H0Z7

Pathways

KEGG R04031 BioCyc O-SUCCINYLBENZOATE-COA-SYN-RXN