Protein profile

KP13_03281

Succinate dehydrogenase cytochrome b556 subunit

Genome: KpKP13

Gene: AHE45660.1 sdhC Structure source: AlphaFold + ColabFold UniProt A0A0V9SNE0
Amino acids 134
Annotations 9
Features 28
PDB binders 11
Druggability 0.676

Overview

Basic information about this protein and its source genome.

Accession
KP13_03281
Gene
AHE45660.1 sdhC
Status
annotated
Amino acids
134
Structure source
AlphaFold + ColabFold
GO
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: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: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:0000104 Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.

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 (%)
64.567
DEG E-value
2.31e-51
Localization
CytoplasmicMembrane
ColabFold pLDDT
95.01

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 0.676
Structure A0A0V9SNE0
Pocket Pocket 1
P2Rank 0.068
Structure A0A0V9SNE0
Pocket Pocket 1
ColabFold model
FPocket 0.687 · Pocket 1
P2Rank 0.105 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 107 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Gene Ontology (GO)

9
  • 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: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: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:0000104 Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0046872 Binding to a metal ion.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
12 131 NCBIfam TIGR02970 succinate dehydrogenase, cytochrome b556 subunit
12 131 InterPro IPR014314 Succinate dehydrogenase, cytochrome b556 subunit
14 131 CDD cd03499 SQR_TypeC_SdhC
14 131 InterPro IPR014314 Succinate dehydrogenase, cytochrome b556 subunit
14 38 ProSitePatterns PS01000 Succinate dehydrogenase cytochrome b subunit signature 1.
14 38 InterPro IPR018495 Succinate dehydrogenase, cytochrome b subunit, conserved site
33 55 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
33 53 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
77 94 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
114 133 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
11 128 Pfam PF01127 Succinate dehydrogenase/Fumarate reductase transmembrane subunit
11 128 InterPro IPR000701 Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit
1 134 PIRSF PIRSF000178 SDH_cyt_b560
1 134 InterPro IPR014314 Succinate dehydrogenase, cytochrome b556 subunit
6 134 Gene3D G3DSA:1.20.1300.10 Fumarate reductase/succinate dehydrogenase, transmembrane subunit
6 134 InterPro IPR034804 Fumarate reductase/succinate dehydrogenase, transmembrane subunit
6 134 FunFam G3DSA:1.20.1300.10:FF:000005 Succinate dehydrogenase cytochrome b556 subunit
134 134 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
95 114 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
89 102 ProSitePatterns PS01001 Succinate dehydrogenase cytochrome b subunit signature 2.
89 102 InterPro IPR018495 Succinate dehydrogenase, cytochrome b subunit, conserved site
6 134 SUPERFAMILY SSF81343 Fumarate reductase respiratory complex transmembrane subunits
73 94 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
7 129 PANTHER PTHR10978 SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT
7 129 InterPro IPR014314 Succinate dehydrogenase, cytochrome b556 subunit
115 133 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 32 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
54 72 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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_A0A0V9SNE0
AlphaFold full sequence Viewing
ColabFold KP13_03281
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 0.676
3 0.395
4 0.299

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 2.08 0.047
2 1.63 0.027
3 1.43 0.019

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.