Protein profile

VK055_1794

succinyl-CoA synthetase, &beta subunit

Genome: KpATCC43816

Gene: sucC AIK80407.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU59
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Amino acids 388
Annotations 11
Features 26
PDB binders 4
Druggability 0.802

Overview

Basic information about this protein and its source genome.

Accession
VK055_1794
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
sucC AIK80407.1
Status
annotated
Amino acids
388
Structure source
AlphaFold + ColabFold
EC
6.2.1.5
GO
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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
46.615
Human E-value
4.45e-111
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
97.423
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.56

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 0.802
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
Normalized 0.071

Sequence

Primary amino-acid sequence viewer.

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 Features

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

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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_A0A0H3GU59
AlphaFold — — full sequence — Viewing
ColabFold VK055_1794
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
17 0.802
1 0.468

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 6.55 0.332
2 1.87 0.037
3 1.51 0.022

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

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
6XRU
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
6NO5
B3FHP0 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
SIN
5CAE
P53590 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
TUY
6WCV
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.