Protein target profile

VK055_4953

D-lactate dehydrogenase

Genome: KpATCC43816 Gene: AIK83479.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GW01
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Length 581
Pocket druggability 0.995
Metabolic reactions 1
Chokepoint No
Functional annotation 1 EC 13 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.

Main supporting evidence

No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. 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. Second pocket predictor agrees P2Rank predicted binding-site probability 1.00. Review the complete evidence below

Risks to review

Microbiome similarity 151 of 4744 screened genomes (3.2%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.99) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.99, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

Evidence gaps

No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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
3.2% 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
92.95 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 0.995
Structure A0A0H3GW01
Pocket Pocket 1
P2Rank 0.997
Structure A0A0H3GW01
Pocket Pocket 1
ColabFold model
FPocket 0.937 · Pocket 6
P2Rank 0.995 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 151 / 4744 genomes with a hit
Prevalence 3.2%

Cross-references

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

Sequence

UniProt A0A0H3GW01

Pathways

KEGG R00704 BioCyc DLACTDEHYDROGNAD-RXN

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways
Pyruvate metabolism
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSSAPTDTHKTFLADLARLVGPSHLLTDPAKTQRYRKGFRSGQGEALAVVFPGTLLELWRVLNACVDADKIILMQAANTGLTEGSTPNGNDYDREIVIISTLRLDKLHLLDKGEQVLAWPGTTLYSLEKALKPLGREPHSVIGSSCIGASVIGGICNNSGGSLVQRGPAYTEMSLFAQIDADGKLKLVNHLGIDLGSTPEQILSRLDDERISDSDVLHDGRHAHDHDYVTRVRDVDADTPARYNADPDRLFESSGCAGKLAVFAVRLDTFPAEKRQQVFYIGTNQPQVLTEIRRHILAEFQHLPVAGEYMHRDIYDIAEKYGKDTFLMIDKLGTDKMPFFFTMKGRTDAMLEKVSLFKPHFTDRFMQKLGHVFPAHLPERMKTWRDKYEHHLLLKMAGDGIEEAQRWLTEYFQQAEGDFFACTPEEGSKAFLHRFAAAGAAIRYQAVHADEVEDILALDIALRRNDTEWFEHLPPEIDSQLVHKLYYGHFMCHVFHQDYIVRKGVDAHALKEKMLELLKARGAQYPAEHNVGHLYEAPESLQQFYRQNDPTNSMNPGIGKTSKQKYWGEAAPTPASPADPQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 13 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

13
  • GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • 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:0016901 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
  • GO:0019516 OBSOLETE. The chemical reactions and pathways resulting in the conversion of lactate to other compounds, such as pyruvate, with concomitant loss of electrons.
  • 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: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.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • 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:0006089 The chemical reactions and pathways involving lactate, the anion of lactic acid.
  • GO:0031234 The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
  • GO:0004458 Catalysis of the reaction: (R)-lactate + 2 [Fe(III)cytochrome c] = 2 [Fe(II)cytochrome c] + 2 H+ + pyruvate.
  • GO:0102029 Catalysis of the reaction: (R)-lactate + an ubiquinone = pyruvate + an ubiquinol.
  • GO:0048038 Binding to a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
269 353 FunFam G3DSA:3.30.70.610:FF:000001 Quinone-dependent D-lactate dehydrogenase
276 567 SUPERFAMILY SSF55103 FAD-linked oxidases, C-terminal domain
276 567 InterPro IPR016164 FAD-linked oxidase-like, C-terminal
106 268 FunFam G3DSA:3.30.465.10:FF:000015 Quinone-dependent D-lactate dehydrogenase
435 519 Gene3D G3DSA:3.30.1370.20 -
435 519 InterPro IPR016173 D-lactate dehydrogenase, cap domain, subdomain 2
435 519 FunFam G3DSA:3.30.1370.20:FF:000001 Quinone-dependent D-lactate dehydrogenase
547 581 MobiDBLite mobidb-lite consensus disorder prediction
278 567 Pfam PF09330 D-lactate dehydrogenase, membrane binding
278 567 InterPro IPR015409 D-lactate dehydrogenase, membrane binding, C-terminal
10 271 SUPERFAMILY SSF56176 FAD-binding/transporter-associated domain-like
10 271 InterPro IPR036318 FAD-binding, type PCMH-like superfamily
1 103 Gene3D G3DSA:3.30.43.10 -
1 103 InterPro IPR016167 FAD-binding, type PCMH, subdomain 1
355 434 FunFam G3DSA:3.30.70.610:FF:000002 Quinone-dependent D-lactate dehydrogenase
47 168 Pfam PF01565 FAD binding domain
47 168 InterPro IPR006094 FAD linked oxidase, N-terminal
4 569 PIRSF PIRSF000101 D-lactate_dh
4 569 InterPro IPR012256 D-lactate dehydrogenase
106 268 Gene3D G3DSA:3.30.465.10 -
106 268 InterPro IPR016169 FAD-binding, type PCMH, subdomain 2
269 352 Gene3D G3DSA:3.30.70.610 -
269 352 InterPro IPR016172 D-lactate dehydrogenase, cap domain, subdomain 1
353 434 Gene3D G3DSA:3.30.70.610 -
353 434 InterPro IPR016172 D-lactate dehydrogenase, cap domain, subdomain 1
42 272 ProSiteProfiles PS51387 PCMH-type FAD-binding domain profile.
42 272 InterPro IPR016166 FAD-binding domain, PCMH-type
2 103 FunFam G3DSA:3.30.43.10:FF:000005 Quinone-dependent D-lactate dehydrogenase
9 557 PANTHER PTHR43716 D-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL
10 568 Hamap MF_02092 Quinone-dependent D-lactate dehydrogenase [dld].
10 568 InterPro IPR012256 D-lactate dehydrogenase

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
0.995
Likely same site as P2Rank 1 4.1 Å 47 shared residues 92% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #13
0.655
Likely same site as P2Rank 4 1.6 Å 7 shared residues 88% of smaller site
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Surrounding area
Site 3 FPocket #16
0.233
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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
0.997
Likely same site as FPocket 1 4.1 Å 47 shared residues 92% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.037
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Surrounding area
Site 3 P2Rank #3
0.037
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Surrounding area
Site 4 P2Rank #4
0.032
Likely same site as FPocket 13 1.6 Å 7 shared residues 88% of smaller site
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Surrounding area
Site 5 P2Rank #5
0.029
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Surrounding area
Residue sets
UniProt: Binding site:143-143
UniProt: Binding site:150-150
UniProt: Binding site:160-160
UniProt: Binding site:257-257
UniProt: Binding site:262-262
UniProt: Binding site:76-80
UniProt: Binding site:84-85
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_A0A0H3GW01
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4953
ColabFold — — full sequence — Loaded