Protein target profile

KP13_03278

Succinate dehydrogenase iron-sulfur subunit

Genome: KpKP13 Gene: AHE45657.1 sdhB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQA9
Length 238
Pocket druggability 0.437
Direct ligand evidence 0 95 total records
Functional annotation 1 EC 10 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

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 (%)
68.889 Lower values reduce human off-target concern.
Human E-value
1.16e-42
Gut microbiome similarity
3.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
77.731 Higher values support similarity to known essential genes.
DEG E-value
5.06e-143 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
97.66 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The 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.

FPocket 0.437
Structure A0A0H3GQA9
Pocket Pocket 2
P2Rank 0.109
Structure A0A0H3GQA9
Pocket Pocket 1
ColabFold model
FPocket 0.466 · Pocket 3
P2Rank 0.127 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 178 / 4744 genomes with a hit
Prevalence 3.8%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MKLEFSIYRYNPDVDDAPHMQDYTLEAEEGRDMMLLDALIQLKEKDPSLSFRRSCREGVCGSDGLNMNGKNGLACITPISALNQPGKKIVIRPLPGLPVIRDLVVDMGQFYAQYEKIKPYLLNNGQNPPAREHLQMPEQREKLDGLYECILCACCSTSCPSFWWNPDKFIGPAGLLAAYRFLIDSRDTETSERLDGLSDAFSVFRCHSIMNCVSVCPKGLNPTRAIGHIKSMLLQRSA

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: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: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: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:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0051538 Binding to a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0046872 Binding to a metal ion.
  • GO:0008177 Catalysis of the reaction: a quinone + succinate = a quinol + fumarate.
  • GO:0022904 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
1 106 Gene3D G3DSA:3.10.20.30 -
1 106 InterPro IPR012675 Beta-grasp domain superfamily
1 106 FunFam G3DSA:3.10.20.30:FF:000004 Succinate dehydrogenase iron-sulfur subunit
5 111 Pfam PF13085 2Fe-2S iron-sulfur cluster binding domain
5 111 InterPro IPR025192 Succinate dehydogenase/fumarate reductase N-terminal
149 160 ProSitePatterns PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.
149 160 InterPro IPR017900 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
107 238 Gene3D G3DSA:1.10.1060.10 -
107 238 InterPro IPR009051 Alpha-helical ferredoxin
107 236 SUPERFAMILY SSF46548 alpha-helical ferredoxin
1 106 SUPERFAMILY SSF54292 2Fe-2S ferredoxin-like
1 106 InterPro IPR036010 2Fe-2S ferredoxin-like superfamily
1 97 ProSiteProfiles PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
1 97 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
7 230 NCBIfam TIGR00384 succinate dehydrogenase and fumarate reductase iron-sulfur protein
7 230 InterPro IPR004489 Succinate dehydrogenase/fumarate reductase iron-sulphur protein
139 169 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
139 169 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
3 235 PANTHER PTHR11921 SUCCINATE DEHYDROGENASE IRON-SULFUR PROTEIN
107 238 FunFam G3DSA:1.10.1060.10:FF:000001 Succinate dehydrogenase iron-sulfur subunit SdhB
148 221 Pfam PF13534 4Fe-4S dicluster domain

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.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #2
0.437
Likely same site as P2Rank 2 1.6 Å 8 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #3
0.239
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.109
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.082
Likely same site as FPocket 2 1.6 Å 8 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.009
Likely same site as FPocket 2 7.8 Å 2 shared residues 25% of smaller site
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental 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_A0A0H3GQA9
AlphaFold DB full sequence Viewing
ColabFold KP13_03278
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.

95 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 45 records from similar proteins
Structural ligands 45 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
11J PDB via homolog 399.2 Da · LogP 5.21 · TPSA 29.1 Open detail RCSB PDB
12J PDB via homolog Detail RCSB PDB
3NP PDB via homolog Detail RCSB PDB
3PE PDB via homolog Detail RCSB PDB
4YP PDB via homolog Detail RCSB PDB

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
11J RCSB PDB Q007T0 399.2 Da LogP 5.21 TPSA 29.1 1 viol. ✓ Clean c1ccc(cc1)c2cccc(c2)NC(=O)c3ccccc3I
12J RCSB PDB O44074 381.2 Da LogP 4.33 TPSA 38.3 ✓ Ro5 ✓ Clean CC(C)Oc1cccc(c1)NC(=O)c2ccccc2I
3NP RCSB PDB Q007T0 119.1 Da LogP -0.26 TPSA 80.4 ✓ Ro5 ✓ Clean C(C[N+](=O)[O-])C(=O)O
3PE RCSB PDB Q9YHT2 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
4YP RCSB PDB O44074 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 RCSB PDB P07014 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 RCSB PDB Q007T0 323.1 Da LogP 3.54 TPSA 29.1 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)c2ccccc2I
BRS RCSB PDB P0AC47 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 RCSB PDB P07014 235.3 Da LogP 2.62 TPSA 38.3 ✓ Ro5 ✓ Clean CC1=C(SCCO1)C(=O)Nc2ccccc2
CDN RCSB PDB P07014 1151.5 Da LogP 14.77 TPSA 249.6 4 viol. ✓ Clean CCCCCCCCCCCCCCC(O)O[C@H](COC(CCCCC)O)CO[P@@](=O…
CE1 RCSB PDB P0AC47 538.8 Da LogP 4.03 TPSA 94.1 1 viol. ✓ Clean CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCOCCO
DNT RCSB PDB P07014 282.3 Da LogP 3.89 TPSA 106.5 ✓ Ro5 ✓ Clean CCCCCC(C)c1cc(cc(c1O)[N+](=O)[O-])[N+](=O)[O-]
E23 RCSB PDB O44074 335.4 Da LogP 4.93 TPSA 29.1 ✓ Ro5 ✓ Clean CC(C)(C)c1ccc(cc1)CNC(=O)c2ccccc2C(F)(F)F
E24 RCSB PDB O44074 348.2 Da LogP 4.94 TPSA 29.1 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)NCc2ccc(cc2Cl)Cl)C(F)(F)F
EBM RCSB PDB Q007T0 289.1 Da LogP 2.43 TPSA 29.1 ✓ Ro5 ✓ Clean CC(C)NC(=O)c1ccccc1I
EPH RCSB PDB P07014 709.9 Da LogP 10.16 TPSA 134.4 2 viol. ✓ Clean CCCC=CCC=CCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCC=CCC…
F3S RCSB PDB P07014 295.8 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]2S[Fe]3[S]2[Fe]1S3
F6A RCSB PDB Q007T0 341.3 Da LogP 5.62 TPSA 29.1 1 viol. ✓ Clean c1ccc(cc1)c2cccc(c2)NC(=O)c3ccccc3C(F)(F)F
F7A RCSB PDB Q007T0 357.3 Da LogP 5.75 TPSA 38.3 1 viol. ✓ Clean c1ccc(cc1)Oc2cccc(c2)NC(=O)c3ccccc3C(F)(F)F
F9A RCSB PDB Q007T0 322.3 Da LogP 4.02 TPSA 32.3 ✓ Ro5 ✓ Clean CN(C)Cc1cccc(c1)NC(=O)c2ccccc2C(F)(F)F
FD8 RCSB PDB Q007T0 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 RCSB PDB P07014 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FLC RCSB PDB P0AC47 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
FTN RCSB PDB Q007T0 323.3 Da LogP 4.74 TPSA 38.3 ✓ Ro5 ✓ Clean CC(C)Oc1cccc(c1)NC(=O)c2ccccc2C(F)(F)F
FUM RCSB PDB O44074 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
GUA RCSB PDB P0AC47 132.1 Da LogP 0.33 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)CC(=O)O
HQO RCSB PDB P0AC47 259.3 Da LogP 3.69 TPSA 47.2 ✓ Ro5 Alert CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
JMP RCSB PDB Q007T0 299.3 Da LogP 3.42 TPSA 75.6 ✓ Ro5 ✓ Clean CC(C)Oc1cccc(c1)NC(=O)c2ccccc2C(=O)O
LMT RCSB PDB T2G9X8 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
MLI RCSB PDB Q007T0 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
MQ7 RCSB PDB P0AC47 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 RCSB PDB Q007T0 269.3 Da LogP 4.03 TPSA 38.3 ✓ Ro5 ✓ Clean Cc1ccccc1C(=O)Nc2cccc(c2)OC(C)C
N1M RCSB PDB Q007T0 261.1 Da LogP 1.65 TPSA 29.1 ✓ Ro5 ✓ Clean CNC(=O)c1ccccc1I
NBI RCSB PDB Q007T0 242.2 Da LogP 2.85 TPSA 72.2 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)c2ccccc2[N+](=O)[O-]
OAA RCSB PDB P07014 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]
PCI RCSB PDB P07014 266.3 Da LogP 4.66 TPSA 20.2 ✓ Ro5 ✓ Clean c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)O
RQX RCSB PDB O44074 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 RCSB PDB Q007T0 213.2 Da LogP 2.64 TPSA 49.3 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)c2ccccc2O
TEO RCSB PDB P07014 132.1 Da LogP -3.14 TPSA 103.7 ✓ Ro5 ✓ Clean C(=C(\O)/[O-])\[C@H](C(=O)[O-])O
TFZ RCSB PDB Q007T0 265.2 Da LogP 3.96 TPSA 29.1 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)c2ccccc2C(F)(F)F
TMG RCSB PDB Q007T0 201.3 Da LogP 2.69 TPSA 41.6 ✓ Ro5 ✓ Clean c1ccc2c(c1)[nH]c(n2)c3cscn3
TTF RCSB PDB Q9YHT2 222.2 Da LogP 2.45 TPSA 34.1 ✓ Ro5 ✓ Clean c1cc(sc1)C(=O)CC(=O)C(F)(F)F
UMQ RCSB PDB Q9YHT2 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 RCSB PDB Q007T0 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 RCSB PDB P07014 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.