Protein target profile

VK055_1794

succinyl-CoA synthetase, &beta subunit

Genome: KpATCC43816 Gene: AIK80407.1 sucC 3D evidence: AlphaFold DB model + ColabFold model Metabolism 3 reactions UniProt A0A0H3GU59
Length 388
Pocket druggability 0.802
Metabolic reactions 3
Chokepoint No
Direct ligand evidence 0 42 total records
Functional annotation 1 EC 10 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.

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 (%)
46.615 Lower values reduce human off-target concern.
Human E-value
4.45e-111
Gut microbiome similarity
7.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
97.423 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.56 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.802
Structure A0A0H3GU59
Pocket Pocket 17
P2Rank 0.658
Structure A0A0H3GU59
Pocket Pocket 1
ColabFold model
FPocket 0.482 · Pocket 10
P2Rank 0.681 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 337 / 4744 genomes with a hit
Prevalence 7.1%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 95.8% of genes in this genome.

Relative network centrality 95.8% more central than 95.8% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reactions

3 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MNLHEYQAKQLFARYGLPAPVGYACTTPREAEEAASKIGAGPWVVKCQVHAGGRGKAGGVKVVKSKEEIRAFAEHWLGKRLVTYQTDANGQPVNQILVEAATDIDKELYLGAVVDRSSRRVVFMASTEGGVEIEKVAEETPHLIHKIAIDPLAGPMPYQGRELAFKLGLEGKQVQQFTKIFMGLATIFLERDLALIEINPLVITKQGDLICLDGKLGADGNALFRQPDLREMRDQSQEDPREAQAAQWELNYVALDGNIGCMVNGAGLAMGTMDIVKLHGGEPANFLDVGGGATKERVTEAFKIILSDDNVKAVLVNIFGGIVRCDLIADGIIGAVAEVGVNVPVVVRLEGNNAELGAKKLADSGLNIIAAKSLTDAAQQVVAAVEGK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
  • GO:0046872 Binding to a metal ion.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0042709 A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP or GTP.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0004775 Catalysis of the reaction: ATP + succinate + CoA = ADP + succinyl-CoA + phosphate.
  • GO:0004776 Catalysis of the reaction: GTP + succinate + CoA = GDP + succinyl-CoA + phosphate.
  • GO:0006104 The chemical reactions and pathways involving succinyl-CoA, a compound composed of the monovalent acyl group 3-carboxypropanoyl, derived from succinic acid by loss of one OH group, linked to coenzyme A.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
92 237 FunFam G3DSA:3.30.470.20:FF:000002 Succinate--CoA ligase [ADP-forming] subunit beta
2 203 Pfam PF08442 ATP-grasp domain
2 203 InterPro IPR013650 ATP-grasp fold, succinyl-CoA synthetase-type
240 388 Gene3D G3DSA:3.40.50.261 -
240 388 InterPro IPR016102 Succinyl-CoA synthetase-like
21 104 Gene3D G3DSA:3.30.1490.20 -
21 104 InterPro IPR013815 ATP-grasp fold, subdomain 1
1 237 Gene3D G3DSA:3.30.470.20 -
1 388 PIRSF PIRSF001554 SucCS_beta
1 388 InterPro IPR005809 Succinate--CoA synthetase, beta subunit
1 385 PANTHER PTHR11815 SUCCINYL-COA SYNTHETASE BETA CHAIN
1 385 InterPro IPR005809 Succinate--CoA synthetase, beta subunit
239 385 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains
239 385 InterPro IPR016102 Succinyl-CoA synthetase-like
21 104 FunFam G3DSA:3.30.1490.20:FF:000002 Succinate--CoA ligase [ADP-forming] subunit beta
1 385 NCBIfam TIGR01016 succinate-CoA ligase subunit beta
1 386 Hamap MF_00558 Succinate--CoA ligase [ADP-forming] subunit beta [sucC].
1 386 InterPro IPR005809 Succinate--CoA synthetase, beta subunit
240 388 FunFam G3DSA:3.40.50.261:FF:000001 Succinate--CoA ligase [ADP-forming] subunit beta
257 282 ProSitePatterns PS01217 ATP-citrate lyase / succinyl-CoA ligases family signature 3.
257 282 InterPro IPR017866 Succinyl-CoA synthetase, beta subunit, conserved site
262 382 Pfam PF00549 CoA-ligase
262 382 InterPro IPR005811 ATP-citrate lyase/succinyl-CoA ligase
9 229 ProSiteProfiles PS50975 ATP-grasp fold profile.
9 229 InterPro IPR011761 ATP-grasp fold
1 238 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-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 · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #17
0.802
Likely same site as P2Rank 1 7.9 Å 11 shared residues 85% of smaller site
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Surrounding area
Site 2 FPocket #1
0.468
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.658
Likely same site as FPocket 17 7.9 Å 11 shared residues 85% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.062
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Surrounding area
Residue sets
UniProt: Binding site:102-102
UniProt: Binding site:107-107
UniProt: Binding site:199-199
UniProt: Binding site:213-213
UniProt: Binding site:264-264
UniProt: Binding site:321-323
UniProt: Binding site:46-46
UniProt: Binding site:53-55
UniProt: Binding site:99-99
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_A0A0H3GU59
AlphaFold DB full sequence Viewing
ColabFold VK055_1794
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.

42 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 38 similarity-based ZINC candidates
Best available ligand signal
DCA PDB via homolog 735.5 Da · LogP -1.58 · TPSA 346.6 Open detail RCSB PDB
NH4 PDB via homolog Detail RCSB PDB
SIN PDB via homolog Detail RCSB PDB
TUY PDB via homolog Detail RCSB PDB
ZINC1532902 ZINC proposed compound · Tanimoto 0.700 Detail ZINC

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
DCA RCSB PDB P53590 735.5 Da LogP -1.58 TPSA 346.6 3 viol. ✓ Clean CCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@@](=O)(O)O[P…
NH4 RCSB PDB B3FHP0 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
SIN RCSB PDB P53590 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
TUY RCSB PDB Q96I99 899.6 Da LogP -3.53 TPSA 441.4 3 viol. ✓ Clean CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([…

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.