Protein target profile

KP13_03277

2-oxoglutarate dehydrogenase E1 component

Genome: KpKP13 Gene: sucA AHE45656.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQ15
Length 935
Pocket druggability 0.729
Direct ligand evidence 0 60 total records
Functional annotation 1 EC 6 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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 (%)
47.101 Lower values reduce human off-target concern.
Human E-value
1.94e-39
Gut microbiome similarity
4.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
93.797 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
93.66 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 0.729
Structure A0A0H3GQ15
Pocket Pocket 49
P2Rank 0.835
Structure A0A0H3GQ15
Pocket Pocket 1
ColabFold model
FPocket 0.606 · Pocket 59
P2Rank 0.876 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 195 / 4744 genomes with a hit
Prevalence 4.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MQNGAMKAWLDSSYLSGSNQSWIEQLYEDFLTDPDSVDANWRSMFQQLPGTGVKPDQFHSKTRDYFRRLAKDASRYTSSISDPDTNVKQVKVLQLINAYRFRGHQHANLDPLGLWKQERVADLDPAYHDLTEADFQESYNVGSFAIGKDTMKLGELIAALKQTYCGSIGAEYMHITSTEEKRWIQQRIESVAGKASFTAEEKKRFLSELTAAEGLERYLGAKFPGAKRFSLEGGDALIPMLKEMIRHAGKSGTREVVLGMAHRGRLNVLVNVLGKKPQDLFDEFAGKHKEHLGTGDVKYHMGFSSDMETEGGLVHLALAFNPSHLEIVSPVVIGSVRARLDRLDEPSSNKVLPITIHGDAAVTGQGVVQETLNMSKARGYEVGGTVRIVINNQVGFTTSNPLDARSTPYCTDIGKMVQAPIFHVNADDPEAVAFVTRLALDFRNTFKRDVFIDLVCYRRHGHNEADEPSATQPLMYQKIKKHPTPRKIYADKLEQEKVATLEDATEQVNLYRDALDAGECVVQEWRPMNMHSFTWSPYLNHEWDESYPDKVEPKRLQELAKRISTVPEGIEMQSRVAKIYADRQAMAAGEKLFDWGGAENLAYATLVDEGIPVRLSGEDSGRGTFFHRHAVIHNQTNGSTYTPLQHVHNGQGQFRVWDSVLSEEAVLAFEYGYATAEPRTLTIWEAQFGDFANGAQVVIDQFISSGEQKWGRMCGLVMLLPHGYEGQGPEHSSARLERYLQLCAEQNMQVCVPSTPAQVYHMLRRQALRGMRRPLVVMSPKSLLRHPLAVSSMDELANGTFLPAIGEIDQLDPQAVKRVVLCSGKVYYDLLEQRRKNEQKDVAIVRIEQLYPFPHQAVQEALKAYAHVHDFVWCQEEPLNQGAWYCSQHHFREVIPFGASLRYAGRPASASPAVGYMSVHQKQQQDLVNDALNVD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0016624 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide.
  • GO:0004591 Catalysis of the reaction: N(6)-[(R)-lipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + 2-oxoglutarate + H+ = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + CO2.
  • GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0045252 A multi-enzyme complex that catalyzes the oxidative decarboxylation of alpha-ketoglutarate (also known as 2-oxoglutarate) to form succinyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
593 787 Pfam PF02779 Transketolase, pyrimidine binding domain
593 787 InterPro IPR005475 Transketolase-like, pyrimidine-binding domain
12 50 Pfam PF16078 2-oxoglutarate dehydrogenase N-terminus
12 50 InterPro IPR032106 2-oxoglutarate dehydrogenase E1 component, N-terminal domain
1 934 PIRSF PIRSF000157 Oxoglu_dh_E1
1 934 InterPro IPR011603 2-oxoglutarate dehydrogenase E1 component
84 166 Gene3D G3DSA:1.10.287.1150 TPP helical domain
576 793 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
576 793 InterPro IPR029061 Thiamin diphosphate-binding fold
215 476 CDD cd02016 TPP_E1_OGDC_like
828 848 Coils Coil Coil
790 932 Pfam PF16870 2-oxoglutarate dehydrogenase C-terminal
790 932 InterPro IPR031717 Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal
14 932 NCBIfam TIGR00239 2-oxoglutarate dehydrogenase E1 component
14 932 InterPro IPR011603 2-oxoglutarate dehydrogenase E1 component
555 802 Gene3D G3DSA:3.40.50.12470 -
791 931 FunFam G3DSA:3.40.50.11610:FF:000001 2-oxoglutarate dehydrogenase E1 component
167 533 FunFam G3DSA:3.40.50.970:FF:000014 2-oxoglutarate dehydrogenase E1 component
167 533 Gene3D G3DSA:3.40.50.970 -
12 932 PANTHER PTHR23152 2-OXOGLUTARATE DEHYDROGENASE
12 932 InterPro IPR011603 2-oxoglutarate dehydrogenase E1 component
723 931 Gene3D G3DSA:3.40.50.11610 -
723 931 InterPro IPR042179 Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily
221 506 Pfam PF00676 Dehydrogenase E1 component
221 506 InterPro IPR001017 Dehydrogenase, E1 component
593 786 SMART SM00861 Transket_pyr_3
593 786 InterPro IPR005475 Transketolase-like, pyrimidine-binding domain
84 166 FunFam G3DSA:1.10.287.1150:FF:000004 2-oxoglutarate dehydrogenase E1 component
555 726 FunFam G3DSA:3.40.50.12470:FF:000002 2-oxoglutarate dehydrogenase E1 component
120 548 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
120 548 InterPro IPR029061 Thiamin diphosphate-binding fold

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 #49
0.729
Likely same site as P2Rank 5 2.4 Å 10 shared residues 91% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #50
0.673
Likely same site as P2Rank 1 2.0 Å 19 shared residues 90% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.835
Likely same site as FPocket 50 2.0 Å 19 shared residues 90% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.815
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.44
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.393
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.278
Likely same site as FPocket 49 2.4 Å 10 shared residues 91% 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_A0A0H3GQ15
AlphaFold DB full sequence Viewing
ColabFold KP13_03277
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.

60 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 10 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
DW3 PDB via homolog 60.1 Da · LogP -0.82 · TPSA 37.3 Open detail RCSB PDB
JQ5 PDB via homolog Detail RCSB PDB
OAA PDB via homolog Detail RCSB PDB
QSP PDB via homolog Detail RCSB PDB
TD6 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
DW3 RCSB PDB A0A3Q0L1E1 60.1 Da LogP -0.82 TPSA 37.3 ✓ Ro5 ✓ Clean C(C=O)O
JQ5 RCSB PDB A0R2B1 210.1 Da LogP 0.60 TPSA 100.9 ✓ Ro5 ✓ Clean CCOP(=O)(C(=O)CCC(=O)O)O
OAA RCSB PDB P0AFG3 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]
QSP RCSB PDB A0R2B1 608.4 Da LogP 0.82 TPSA 283.4 3 viol. ✓ Clean Cc1ncc(c(n1)N)CN2[C@H](SC(=C2C)CCOP(=O)(O)OP(=O…
TD6 RCSB PDB A0R2B1 527.4 Da LogP 0.74 TPSA 226.5 2 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](CCC(=O)O)O)CCO…
TD7 RCSB PDB A0R2B1 526.4 Da LogP 2.36 TPSA 225.9 3 viol. ✓ Clean Cc1ncc(c(n1)N)CN2C(=C(SC2=C(CCC(=O)O)O)CCO[P@](…
TD8 RCSB PDB A0R2B1 541.4 Da LogP 1.13 TPSA 226.5 2 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@H](CCCC(=O)O)O)C…
TD9 RCSB PDB A0R2B1 541.4 Da LogP 1.13 TPSA 226.5 2 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](CCCC(=O)O)O)CC…
TDW RCSB PDB A0R2B1 469.4 Da LogP 0.90 TPSA 189.2 ✓ Ro5 ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](C)O)CCOP(=O)(O…
ZP1 RCSB PDB A0R2B1 636.5 Da LogP 1.87 TPSA 272.4 3 viol. ✓ Clean CCOP(=O)([C@@](CCC(=O)O)([C@@H]1N(C(=C(S1)CCOP(…

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.