Protein profile

KP13_03279

Succinate dehydrogenase flavoprotein subunit

Genome: KpKP13

Gene: AHE45658.1 sdhA Structure source: AlphaFold + ColabFold UniProt A0A0H3GU54
Amino acids 588
Annotations 10
Features 30
PDB binders 41
Druggability 0.582

Overview

Basic information about this protein and its source genome.

Accession
KP13_03279
Gene
AHE45658.1 sdhA
Status
annotated
Amino acids
588
Structure source
AlphaFold + ColabFold
EC
GO
GO:0022900 A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors. 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. 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:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
63.514
Human E-value
1.69e-120
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
97.449
DEG E-value
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
98.44

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 0.582
Structure A0A0H3GU54
Pocket Pocket 27
P2Rank 0.968
Structure A0A0H3GU54
Pocket Pocket 1
ColabFold model
FPocket 0.895 · Pocket 1
P2Rank 0.977 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 177 / 4744 genomes with a hit
Normalized 0.037

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0022900 A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors.
  • 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.
  • 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:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • 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:0008177 Catalysis of the reaction: a quinone + succinate = a quinol + fumarate.
  • GO:0009061 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
1 579 PIRSF PIRSF000171 SDHA_APRA_LASPO
246 350 Gene3D G3DSA:3.90.700.10 Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
246 350 InterPro IPR027477 Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily
548 588 FunFam G3DSA:4.10.80.40:FF:000001 Succinate dehydrogenase flavoprotein subunit
452 588 SUPERFAMILY SSF46977 Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain
452 588 InterPro IPR037099 Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily
43 52 ProSitePatterns PS00504 Fumarate reductase / succinate dehydrogenase FAD-binding site.
43 52 InterPro IPR003952 Fumarate reductase/succinate dehydrogenase, FAD-binding site
246 350 FunFam G3DSA:3.90.700.10:FF:000001 Mitochondrial succinate dehydrogenase flavoprotein subunit
548 588 Gene3D G3DSA:4.10.80.40 succinate dehydrogenase protein domain
431 547 Gene3D G3DSA:1.20.58.100 -
9 416 Gene3D G3DSA:3.50.50.60 -
9 416 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
6 588 PANTHER PTHR11632 SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT
6 588 InterPro IPR030664 FAD-dependent oxidoreductase SdhA/FrdA/AprA
236 356 SUPERFAMILY SSF56425 Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
236 356 InterPro IPR027477 Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily
460 588 Pfam PF02910 Fumarate reductase flavoprotein C-term
460 588 InterPro IPR015939 Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal
9 588 NCBIfam TIGR01812 succinate dehydrogenase or fumarate reductase, flavoprotein subunit
9 588 InterPro IPR014006 Succinate dehydrogenase/fumarate reductase, flavoprotein subunit
4 439 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
4 439 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
9 405 Pfam PF00890 FAD binding domain
9 405 InterPro IPR003953 FAD-dependent oxidoreductase 2, FAD binding domain
6 588 NCBIfam TIGR01816 succinate dehydrogenase flavoprotein subunit
6 588 InterPro IPR011281 Succinate dehydrogenase, flavoprotein subunit
431 547 FunFam G3DSA:1.20.58.100:FF:000001 Succinate dehydrogenase flavoprotein subunit (SdhA)
10 29 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
368 390 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature

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_A0A0H3GU54
AlphaFold full sequence Viewing
ColabFold KP13_03279
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
27 0.582
16 0.37
29 0.216

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 26.66 0.916
2 12.68 0.658
3 2.59 0.074
4 2.1 0.048
5 1.96 0.041

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.

91 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
12J Q33862 381.2 Da LogP 4.33 TPSA 38.3 ✓ Ro5 ✓ Clean CC(C)Oc1cccc(c1)NC(=O)c2ccccc2I
3NP P00363 119.1 Da LogP -0.26 TPSA 80.4 ✓ Ro5 ✓ Clean C(C[N+](=O)[O-])C(=O)O
3PE Q9YHT1 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
4YP Q33862 303.4 Da LogP 3.35 TPSA 69.4 ✓ Ro5 Alert CC1=C(C(=O)C(=C(C1=O)N)OC)C/C=C(\C)/CCC=C(C)C
AT5 P0AC41 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)[…
BOL Q0QF01 323.1 Da LogP 3.54 TPSA 29.1 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)c2ccccc2I
BRS P00363 322.7 Da LogP 4.01 TPSA 106.5 ✓ Ro5 ✓ Clean C[C@H](c1ccc(cc1)Cl)c2cc(cc(c2O)[N+](=O)[O-])[N…
CBE P0AC41 235.3 Da LogP 2.62 TPSA 38.3 ✓ Ro5 ✓ Clean CC1=C(SCCO1)C(=O)Nc2ccccc2
CDN P0AC41 1151.5 Da LogP 14.77 TPSA 249.6 4 viol. ✓ Clean CCCCCCCCCCCCCCC(O)O[C@H](COC(CCCCC)O)CO[P@@](=O…
CE1 P00363 538.8 Da LogP 4.03 TPSA 94.1 1 viol. ✓ Clean CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCOCCO
DNT P0AC41 282.3 Da LogP 3.89 TPSA 106.5 ✓ Ro5 ✓ Clean CCCCCC(C)c1cc(cc(c1O)[N+](=O)[O-])[N+](=O)[O-]
E23 Q33862 335.4 Da LogP 4.93 TPSA 29.1 ✓ Ro5 ✓ Clean CC(C)(C)c1ccc(cc1)CNC(=O)c2ccccc2C(F)(F)F
E24 Q33862 348.2 Da LogP 4.94 TPSA 29.1 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)NCc2ccc(cc2Cl)Cl)C(F)(F)F
EPH P0AC41 709.9 Da LogP 10.16 TPSA 134.4 2 viol. ✓ Clean CCCC=CCC=CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCC=CCC…
F3S P0AC41 295.8 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]2S[Fe]3[S]2[Fe]1S3
F6A Q33862 341.3 Da LogP 5.62 TPSA 29.1 1 viol. ✓ Clean c1ccc(cc1)c2cccc(c2)NC(=O)c3ccccc3C(F)(F)F
F7A Q0QF01 357.3 Da LogP 5.75 TPSA 38.3 1 viol. ✓ Clean c1ccc(cc1)Oc2cccc(c2)NC(=O)c3ccccc3C(F)(F)F
F9A Q0QF01 322.3 Da LogP 4.02 TPSA 32.3 ✓ Ro5 ✓ Clean CN(C)Cc1cccc(c1)NC(=O)c2ccccc2C(F)(F)F
FD8 Q33862 447.3 Da LogP 6.45 TPSA 38.3 1 viol. ✓ Clean c1ccc(c(c1)C(=O)Nc2cccc(c2)Oc3c(c(c(c(c3F)F)F)F…
FES P0AC41 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FLC P00363 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
FTN Q33862 323.3 Da LogP 4.74 TPSA 38.3 ✓ Ro5 ✓ Clean CC(C)Oc1cccc(c1)NC(=O)c2ccccc2C(F)(F)F
FUM Q33862 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
GUA P00363 132.1 Da LogP 0.33 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)CC(=O)O
HQO P00363 259.3 Da LogP 3.69 TPSA 47.2 ✓ Ro5 Alert CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
MLI Q33862 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
MQ7 P00363 649.0 Da LogP 14.10 TPSA 34.1 2 viol. Alert CC1=C(C(=O)c2ccccc2C1=O)C\C=C(/C)\CC\C=C(/C)\CC…
MRN Q33862 269.3 Da LogP 4.03 TPSA 38.3 ✓ Ro5 ✓ Clean Cc1ccccc1C(=O)Nc2cccc(c2)OC(C)C
N1M Q0QF01 261.1 Da LogP 1.65 TPSA 29.1 ✓ Ro5 ✓ Clean CNC(=O)c1ccccc1I
OAA P0AC41 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]
PBF P00363 269.3 Da LogP 1.87 TPSA 80.4 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)c2ccc(cc2)C[C@@H](C(=O)O)N
PCI P0AC41 266.3 Da LogP 4.66 TPSA 20.2 ✓ Ro5 ✓ Clean c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)O
RQX Q33862 263.3 Da LogP 2.41 TPSA 69.4 ✓ Ro5 Alert CCC/C(=C/CC1=C(C(=O)C(=C(C1=O)OC)N)C)/C
SLI Q0QF01 213.2 Da LogP 2.64 TPSA 49.3 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)c2ccccc2O
TEO P0AC41 132.1 Da LogP -3.14 TPSA 103.7 ✓ Ro5 ✓ Clean C(=C(\O)/[O-])\[C@H](C(=O)[O-])O
TFZ Q0QF01 265.2 Da LogP 3.96 TPSA 29.1 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)c2ccccc2C(F)(F)F
TMG Q0QF01 201.3 Da LogP 2.69 TPSA 41.6 ✓ Ro5 ✓ Clean c1ccc2c(c1)[nH]c(n2)c3cscn3
TTF Q0QF01 222.2 Da LogP 2.45 TPSA 34.1 ✓ Ro5 ✓ Clean c1cc(sc1)C(=O)CC(=O)C(F)(F)F
UMQ Q9YHT1 496.6 Da LogP -0.84 TPSA 178.5 2 viol. ✓ Clean CCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)…
UQ1 Q33862 250.3 Da LogP 2.32 TPSA 52.6 ✓ Ro5 Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)CC=C(C)C
UQ2 P0AC41 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.