Protein profile

VK055_1800

succinate dehydrogenase, cytochrome b556 subunit

Genome: KpATCC43816

Gene: AIK80413.1 sdhC Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ10
Amino acids 91
Annotations 7
Features 26
PDB binders 11
Druggability 0.906

Overview

Basic information about this protein and its source genome.

Accession
VK055_1800
Gene
AIK80413.1 sdhC
Status
annotated
Amino acids
91
Structure source
AlphaFold + ColabFold
GO
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0016627 Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. GO:0045281 OBSOLETE. A multimeric complex which consists of flavoprotein (subunit A ; InterPro:IPR003952), iron-sulfur protein (subunit B) and membrane-bound cytochrome b560 (subunit C; InterPro:IPR000701). In some Archaea, the membrane-bound subunits (C or C and D) do not necessarily contain heme. Membrane-bound subunits can bind or react with quinones. GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways. GO:0000104 Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
57.778
DEG E-value
4.52e-28
Localization
CytoplasmicMembrane
ColabFold pLDDT
97.38

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 0.906
Structure A0A0H3GQ10
Pocket Pocket 1
P2Rank 0.029
Structure A0A0H3GQ10
Pocket Pocket 1
ColabFold model
FPocket 0.674 · Pocket 1
P2Rank 0.043 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 122 / 4744 genomes with a hit
Normalized 0.026

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0016627 Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
  • GO:0045281 OBSOLETE. A multimeric complex which consists of flavoprotein (subunit A ; InterPro:IPR003952), iron-sulfur protein (subunit B) and membrane-bound cytochrome b560 (subunit C; InterPro:IPR000701). In some Archaea, the membrane-bound subunits (C or C and D) do not necessarily contain heme. Membrane-bound subunits can bind or react with quinones.
  • GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
  • GO:0000104 Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
71 90 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 15 SignalP_EUK SignalP-TM SignalP-TM
3 91 SUPERFAMILY SSF81343 Fumarate reductase respiratory complex transmembrane subunits
3 91 InterPro IPR034804 Fumarate reductase/succinate dehydrogenase, transmembrane subunit
31 51 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
16 30 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
2 88 NCBIfam TIGR02970 succinate dehydrogenase, cytochrome b556 subunit
2 88 InterPro IPR014314 Succinate dehydrogenase, cytochrome b556 subunit
5 27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
11 15 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 15 Phobius SIGNAL_PEPTIDE Signal peptide region
2 88 CDD cd03499 SQR_TypeC_SdhC
91 91 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
34 56 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 91 PIRSF PIRSF000178 SDH_cyt_b560
1 91 InterPro IPR014314 Succinate dehydrogenase, cytochrome b556 subunit
72 90 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
4 85 Pfam PF01127 Succinate dehydrogenase/Fumarate reductase transmembrane subunit
4 85 InterPro IPR000701 Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit
46 59 ProSitePatterns PS01001 Succinate dehydrogenase cytochrome b subunit signature 2.
46 59 InterPro IPR018495 Succinate dehydrogenase, cytochrome b subunit, conserved site
52 71 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
2 10 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 91 Gene3D G3DSA:1.20.1300.10 Fumarate reductase/succinate dehydrogenase, transmembrane subunit
1 91 InterPro IPR034804 Fumarate reductase/succinate dehydrogenase, transmembrane subunit

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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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_A0A0H3GQ10
AlphaFold full sequence Viewing
ColabFold VK055_1800
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
1 0.906

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 1.53 0.023
2 1.07 0.007

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.

61 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
AT5 P69054 366.2 Da LogP 2.79 TPSA 88.6 ✓ Ro5 ✓ Clean C[C@@H](C[C@H](C)C(=O)C1=C(C(=C(NC1=O)OC)OC)O)[…
CBE P69054 235.3 Da LogP 2.62 TPSA 38.3 ✓ Ro5 ✓ Clean CC1=C(SCCO1)C(=O)Nc2ccccc2
CDN P69054 1151.5 Da LogP 14.77 TPSA 249.6 4 viol. ✓ Clean CCCCCCCCCCCCCCC(O)O[C@H](COC(CCCCC)O)CO[P@@](=O…
DNT P69054 282.3 Da LogP 3.89 TPSA 106.5 ✓ Ro5 ✓ Clean CCCCCC(C)c1cc(cc(c1O)[N+](=O)[O-])[N+](=O)[O-]
EPH P69054 709.9 Da LogP 10.16 TPSA 134.4 2 viol. ✓ Clean CCCC=CCC=CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCC=CCC…
F3S P69054 295.8 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]2S[Fe]3[S]2[Fe]1S3
FES P69054 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
OAA P69054 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]
PCI P69054 266.3 Da LogP 4.66 TPSA 20.2 ✓ Ro5 ✓ Clean c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)O
TEO P69054 132.1 Da LogP -3.14 TPSA 103.7 ✓ Ro5 ✓ Clean C(=C(\O)/[O-])\[C@H](C(=O)[O-])O
UQ2 P69054 318.4 Da LogP 4.04 TPSA 52.6 ✓ Ro5 Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CCC=C(C)C

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.