Protein target profile
VK055_1794
succinyl-CoA synthetase, &beta subunit
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
Risks to review
Evidence coverage
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 modelThe 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.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.
Sequence
Sequence
Primary amino-acid sequence viewer.
MNLHEYQAKQLFARYGLPAPVGYACTTPREAEEAASKIGAGPWVVKCQVHAGGRGKAGGVKVVKSKEEIRAFAEHWLGKRLVTYQTDANGQPVNQILVEAATDIDKELYLGAVVDRSSRRVVFMASTEGGVEIEKVAEETPHLIHKIAIDPLAGPMPYQGRELAFKLGLEGKQVQQFTKIFMGLATIFLERDLALIEINPLVITKQGDLICLDGKLGADGNALFRQPDLREMRDQSQEDPREAQAAQWELNYVALDGNIGCMVNGAGLAMGTMDIVKLHGGEPANFLDVGGGATKERVTEAFKIILSDDNVKAVLVNIFGGIVRCDLIADGIIGAVAEVGVNVPVVVRLEGNNAELGAKKLADSGLNIIAAKSLTDAAQQVVAAVEGK
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene 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.
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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Residue sets
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Residue sets
All structural evidence
Structural evidence
0 + 2Experimental 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.
Structural ligand evidence is available for this target.
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 |
|---|---|---|---|---|---|---|
| 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]([…
|
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 |
|---|---|---|---|---|---|
| ZINC1532902 ZINC | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC2018106 ZINC | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@](O)(CC(=O)O)C(=O)O
|
| ZINC3593496 ZINC | 0.652 | 206.2 Da LogP -1.16 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
COC(=O)C[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC3593497 ZINC | 0.652 | 206.2 Da LogP -1.16 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
COC(=O)C[C@](O)(CC(=O)O)C(=O)O
|
| ZINC14686440 ZINC | 0.625 | 436.4 Da LogP -2.64 TPSA 247.9 | 1 viol. | ✓ Clean |
O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…
|
| ZINC14686442 ZINC | 0.625 | 436.4 Da LogP -2.64 TPSA 247.9 | 1 viol. | ✓ Clean |
O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…
|
| ZINC14686444 ZINC | 0.625 | 436.4 Da LogP -2.64 TPSA 247.9 | 1 viol. | ✓ Clean |
O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…
|
| ZINC3860440 ZINC | 0.615 | 258.4 Da LogP 3.84 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCC(=O)O
|
| ZINC13398039 ZINC | 0.577 | 234.2 Da LogP -0.38 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O
|
| ZINC2528012 ZINC | 0.577 | 234.2 Da LogP -0.38 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=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
|
| ZINC146315135 ZINC | 0.560 | 204.2 Da LogP 0.86 TPSA 94.8 | ✓ Ro5 | ✓ Clean |
CCCCC[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC146315336 ZINC | 0.560 | 204.2 Da LogP 0.86 TPSA 94.8 | ✓ Ro5 | ✓ Clean |
CCCCC[C@](O)(CC(=O)O)C(=O)O
|
| ZINC1850353 ZINC | 0.556 | 206.1 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC(O)(CC(=O)O)CC(=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
|
| ZINC12501123 ZINC | 0.522 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…
|
| ZINC4228234 ZINC | 0.522 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…
|
| ZINC79671662 ZINC | 0.522 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…
|
| ZINC79671663 ZINC | 0.522 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…
|
| ZINC13398014 ZINC | 0.522 | 220.2 Da LogP -1.07 TPSA 110.1 | ✓ Ro5 | ✓ Clean |
COC(=O)CC(O)(CC(=O)OC)C(=O)O
|
| ZINC3861629 ZINC | 0.522 | 206.1 Da LogP -1.16 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
COC(=O)C(O)(CC(=O)O)CC(=O)O
|
| ZINC100969993 ZINC | 0.500 | 359.5 Da LogP 2.70 TPSA 123.9 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCNC(=O)C[C@](O)(CC(=O)O)C(=O)O
|
| ZINC100969996 ZINC | 0.500 | 359.5 Da LogP 2.70 TPSA 123.9 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCNC(=O)C[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC12360002 ZINC | 0.500 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…
|
| ZINC12360703 ZINC | 0.500 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…
|
| ZINC12503599 ZINC | 0.500 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…
|
| ZINC16546165 ZINC | 0.500 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…
|
| ZINC1711854 ZINC | 0.500 | 248.2 Da LogP -0.13 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)CC(CC(=O)O)(CC(=O)O)CC(=O)O
|
| ZINC31977053 ZINC | 0.500 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…
|
| ZINC38682833 ZINC | 0.500 | 286.3 Da LogP -0.61 TPSA 115.2 | ✓ Ro5 | ✓ Clean |
O=C(O)CCC(=O)N1CCN(C(=O)CCC(=O)O)CC1
|
| ZINC4181831 ZINC | 0.500 | 232.2 Da LogP -0.01 TPSA 129.0 | ✓ Ro5 | ✓ Clean |
O=C(O)CCC(=O)C(CC(=O)O)CC(=O)O
|
| ZINC4806433 ZINC | 0.500 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…
|
| ZINC53683898 ZINC | 0.500 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…
|
| ZINC8586019 ZINC | 0.500 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…
|
| ZINC8586020 ZINC | 0.500 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…
|
| ZINC8586021 ZINC | 0.500 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…
|
| ZINC8586022 ZINC | 0.500 | 427.2 Da LogP -1.75 TPSA 232.6 | 2 viol. | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…
|
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.