Protein target profile

KP13_05584

putative pyruvate-flavodoxin oxidoreductase

Genome: KpKP13 Gene: AHE44876.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSL1
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Length 1175
Pocket druggability 0.964
Direct ligand evidence 0 9 total records
Functional annotation 1 EC 8 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.96, P2Rank 0.90). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.96. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 178 of 4744 screened genomes (3.8%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.96) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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
No hit
Gut microbiome similarity
3.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
95.06 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 0.964
Structure A0A0H3GSL1
Pocket Pocket 1
P2Rank 0.895
Structure A0A0H3GSL1
Pocket Pocket 1
ColabFold model
FPocket 0.952 · Pocket 13
P2Rank 0.876 · 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

UniProt A0A0H3GSL1

Sequence

Primary amino-acid sequence viewer.

MITIDGNGAVASVAFRTSEVIAIYPITPSSTMAEQADAWAGNGLKNVWGDVPRVVEMQSEAGAIGAVHGALQTGALSTSFTSSQGLLLMIPTLYKLAGQLMPFVLHVAARTVATHALSIFGDHSDVMAVRQTGCAMLCASSVQEAQDFALISHIATLQSRVPFIHFFDGFRTSHEINKIAPLADDTIRALLPQDKIAEHRQRALNPEHPVIRGTSANPDTYFQSREATNPWYDAVYDHVEKAMDDFAAATGRQYKPFEFYGHPQAERVIVIMGSAIGTCEEVVDELLSRGEKVGVLKVRLYRPFSAAHLLAALPESARAVAVLDRTKEPGALAEPLYLDVMTALAEAFNRGERETLPRTIGGRYGLSSKEFGPECVLAIFSELQAAQPKPRFTVGIYDDVTNLSLPLGENTLPAEAKLEALFYGLGSDGSVSATKNNIKIIGNSTPWFSQGYFVYDSKKAGGLTVSHLRVSEKPIRSSYLISQADFVGCHQLQFIDKYQMAERLKPGGIFLLNTPYSAVEVWSRLPQEVQATLNQKKARFYVVNAAKIARECSLGARINTVMQMAFFHLTQILPGDSALAELQAAIAKSYSSKGQELVERNWQALALARESLAEVPLQPVNASSPNRPPVVSDAAPDFVKTVTAAMLAGLGDALPVSALPPDGTWPMGTTRWEKRNIAEEIPIWKEALCTQCNHCVAACPHSAIRAKVVAPEEMENAPASLHSLDVKSRDMRGQKYVLQVAPEDCTGCNLCVEVCPAKDRQNPEIKAINMMSRLEHVEEEKVNYEYFLNLPEIDRSKLERIDIRTSQLISPLFEYSGACSGCGETPYIKLLTQLYGDRMLIANATGCSSIYGGNLPSTPYTTDANGRGPAWANSLFEDNAEFGLGFRLTVDQHRQRVMRLLSEFADKLPVELNAALHAEATPEVRREQVAALRQALAGVAGAEELLTDADALVEKSVWLIGGDGWAYDIGFGGLDHVLSLTENVNILVLDTQCYSNTGGQASKATPLGAVTKFGEHGKRKARKDLGVSMMMYGHVYVAQISLGAQLNQTVKAIQEAEAYPGPSLIIAYSPCEEHGYDLALSHDQMRQLTATGFWPLYRFDPRRADEGKIPLALDSRPPSDALAETLLNEQRFRRLNAQQPEVAEQLWKDAAADLQKRYDFLAQLAGKAEKSPSEG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • 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: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:0016903 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 hydrogen or electron acceptor.
  • 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:0005506 Binding to an iron (Fe) ion.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • 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:0006979 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

52 records
Show feature table
Start End DB Term Name
736 765 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
736 765 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
631 668 Gene3D G3DSA:4.10.780.10 -
631 668 InterPro IPR037112 Pyruvate-flavodoxin oxidoreductase, EKR domain superfamily
669 791 Gene3D G3DSA:3.30.70.20 -
680 709 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
680 709 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
6 169 CDD cd07034 TPP_PYR_PFOR_IOR-alpha_like
6 169 InterPro IPR002880 Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain
2 254 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
2 254 InterPro IPR029061 Thiamin diphosphate-binding fold
665 838 SUPERFAMILY SSF54862 4Fe-4S ferredoxins
1 1164 PANTHER PTHR32154 PYRUVATE-FLAVODOXIN OXIDOREDUCTASE-RELATED
255 414 Gene3D G3DSA:3.40.50.920 -
255 414 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
419 668 SUPERFAMILY SSF53323 Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
419 668 InterPro IPR002869 Pyruvate-flavodoxin oxidoreductase, central domain
1 1165 NCBIfam TIGR02176 pyruvate:ferredoxin (flavodoxin) oxidoreductase
1 1165 InterPro IPR011895 Pyruvate-flavodoxin oxidoreductase
1 1174 PIRSF PIRSF000159 NifJ
1 1174 InterPro IPR011895 Pyruvate-flavodoxin oxidoreductase
417 623 Gene3D G3DSA:3.40.920.10 -
417 623 InterPro IPR002869 Pyruvate-flavodoxin oxidoreductase, central domain
1 254 Gene3D G3DSA:3.40.50.970 -
689 757 Pfam PF12838 4Fe-4S dicluster domain
689 757 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
1 254 FunFam G3DSA:3.40.50.970:FF:000012 Pyruvate:ferredoxin (Flavodoxin) oxidoreductase
426 610 Pfam PF01558 Pyruvate ferredoxin/flavodoxin oxidoreductase
426 610 InterPro IPR019752 Pyruvate/ketoisovalerate oxidoreductase, catalytic domain
811 1166 CDD cd03377 TPP_PFOR_PNO
794 1167 Gene3D G3DSA:3.40.50.970 -
669 791 FunFam G3DSA:3.30.70.20:FF:000022 Pyruvate:ferredoxin (Flavodoxin) oxidoreductase
794 1166 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
794 1166 InterPro IPR029061 Thiamin diphosphate-binding fold
255 411 SUPERFAMILY SSF52922 TK C-terminal domain-like
255 411 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
622 679 SMART SM00890 EKR_2
622 679 InterPro IPR019456 Pyruvate-flavodoxin oxidoreductase, EKR domain
265 347 Pfam PF17147 Pyruvate:ferredoxin oxidoreductase core domain II
265 347 InterPro IPR033412 Pyruvate:ferredoxin oxidoreductase, core domain II
13 243 Pfam PF01855 Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
13 243 InterPro IPR002880 Pyruvate flavodoxin/ferredoxin oxidoreductase, pyrimidine binding domain
255 413 FunFam G3DSA:3.40.50.920:FF:000007 Pyruvate:ferredoxin (Flavodoxin) oxidoreductase
631 668 FunFam G3DSA:4.10.780.10:FF:000001 Probable pyruvate-flavodoxin oxidoreductase
626 678 Pfam PF10371 Domain of unknown function
626 678 InterPro IPR019456 Pyruvate-flavodoxin oxidoreductase, EKR domain
745 756 ProSitePatterns PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.
745 756 InterPro IPR017900 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
794 1167 FunFam G3DSA:3.40.50.970:FF:000047 Probable pyruvate-flavodoxin oxidoreductase
416 626 FunFam G3DSA:3.40.920.10:FF:000001 Pyruvate:ferredoxin (Flavodoxin) oxidoreductase
936 1066 Pfam PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
936 1066 InterPro IPR011766 Thiamine pyrophosphate enzyme, TPP-binding

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 #1
0.964
Likely same site as P2Rank 1 0.6 Å 26 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #78
0.361
Unusual size
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Surrounding area
Site 3 FPocket #5
0.205
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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
0.895
Likely same site as FPocket 1 0.6 Å 26 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.7
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Surrounding area
Site 3 P2Rank #3
0.561
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Surrounding area
Site 4 P2Rank #4
0.474
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Surrounding area
Site 5 P2Rank #5
0.317
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Surrounding area
Residue sets
UniProt: Binding site:1071-1071
UniProt: Binding site:110-110
UniProt: Binding site:27-27
UniProt: Binding site:60-60
UniProt: Binding site:689-689
UniProt: Binding site:692-692
UniProt: Binding site:695-695
UniProt: Binding site:699-699
UniProt: Binding site:745-745
UniProt: Binding site:748-748
UniProt: Binding site:751-751
UniProt: Binding site:755-755
UniProt: Binding site:819-819
UniProt: Binding site:822-822
UniProt: Binding site:824-824
UniProt: Binding site:847-847
UniProt: Binding site:962-965
UniProt: Binding site:991-996
UniProt: Site:110-110 Important for catalytic activity
UniProt: Site:27-27 Important for catalytic activity
UniProt: Site:60-60 Important for catalytic activity
UniProt: Site:996-996 Important for catalytic activity
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_A0A0H3GSL1
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_05584
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.

9 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 3 similarity-based ZINC candidates
Best available ligand signal
5SR PDB via homolog 468.3 Da · LogP -0.09 · TPSA 209.1 Open detail RCSB PDB
CO2 PDB via homolog Detail RCSB PDB
HTL PDB via homolog Detail RCSB PDB
O2T PDB via homolog Detail RCSB PDB
PYR 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
5SR RCSB PDB
5EXE
Q2RI41 468.3 Da LogP -0.09 TPSA 209.1 ✓ Ro5 ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)O)CCOP(=O)(O)OP…
CO2 RCSB PDB
1KEK
P94692 44.0 Da LogP -0.58 TPSA 34.1 ✓ Ro5 ✓ Clean C(=O)=O
HTL RCSB PDB
1KEK
P94692 467.4 Da LogP 1.04 TPSA 186.0 ✓ Ro5 ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)C)CCO[P@@](=O)(…
O2T RCSB PDB
5EXD
Q2RI41 514.3 Da LogP -1.57 TPSA 249.6 3 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C(=O)O)(O)O)CCOP(=…
PYR RCSB PDB
2C42
P94692 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
TDL RCSB PDB
6CIO
Q2RMD6 513.4 Da LogP 0.13 TPSA 226.5 2 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](C)(C(=O)O)O)CCO…

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.