Protein target profile

VK055_0372

formate dehydrogenase, alpha subunit

Genome: KpATCC43816 Gene: AIK78998.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GR17
Length 716
Pocket druggability 1
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 60 total records
Functional annotation 0 EC 10 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
No hit
Gut microbiome similarity
11.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.65 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 1
Structure A0A0H3GR17
Pocket Pocket 1
P2Rank 0.988
Structure A0A0H3GR17
Pocket Pocket 1
ColabFold model
FPocket 1 · Pocket 1
P2Rank 0.955 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 556 / 4744 genomes with a hit
Prevalence 11.7%

Cross-references

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

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
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.

MKKITSVCPYCGAGCKLKLVVDNNKIIRAEAADGVTNQNQLCLKGYYGWDFLNDTQLLTPRLKQPMIRYQKGGAFTPVSWQEAIRYTASKLKEIKEKHGPRAIMTTGSSRGTGNETNYVMQKFARAVLNTNNVDCCARVCHGPSVAGLQQALGNGAMSNSISDIENSKCLLVFGYNCADSHPIVARRVIKARDNGAKIIVCDPRRIETARIADRHLQLNNGSNMALVNAFGYVLLEEELYNKTYVERYTEGLDAYREAVKDYAPEAVEGIVGVSAREIREAMRMFAAAPSATIMWGMGVTQFGQAVDVVRGLASLALLTGNLGRPNVGVGPVRGQNNVQGACDMGVLPNLFPGYQEVTDPAVRAKFAAAWGIDPALMDDQVGTRITEVPHKALTGEIKAYYIMGEDPLQTEADLGLVRKGIEALDFVVVQDIFMTKTAEMADVLLPATSWGEHGGVFTCADRGFQRFEQAIPPAGNVKRDWEIISLLASELGYPMHYENNQQIWDEMRELCPLFYGVTWEKMGDMGHVQWPCPTLDHPGTPWLYQDNRFDTPSGKGQLFATAWRAPAERPDDEWPLVLCTVREVGHYSCRSMTGNCAALQSLADEPGRVQMNPADAQRLGIADKQLVWVSSRRGKVISRADLSDRINPGAVYMTYQWWVGACNELTQDNLDPISKTPETKYCAVKVEAIADQQWAERYAWTAYSDMKARLKAAADV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Gene Ontology (GO)

10
  • GO:0015942 The chemical reactions and pathways involving formate, also known as methanoate, the anion HCOO- derived from methanoic (formic) acid.
  • 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:0008863 Catalysis of the reaction: formate + NAD+ = CO2 + NADH.
  • GO:0043546 Binding to a molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:1990204 Any protein complex that possesses oxidoreductase activity.
  • 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:0003954 Catalysis of the reaction: NADH + H+ + acceptor = NAD+ + reduced acceptor.
  • 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.

32 records
Show feature table
Start End DB Term Name
1 55 Gene3D G3DSA:2.20.25.90 -
573 689 Gene3D G3DSA:2.40.40.20 -
73 532 Gene3D G3DSA:3.40.50.740 -
535 693 PIRSF PIRSF000144 CbbBc
52 437 PIRSF PIRSF000144 CbbBc
140 334 FunFam G3DSA:3.40.228.10:FF:000002 Formate dehydrogenase subunit alpha
576 683 Pfam PF01568 Molydopterin dinucleotide binding domain
576 683 InterPro IPR006657 Molybdopterin dinucleotide-binding domain
1 564 SUPERFAMILY SSF53706 Formate dehydrogenase/DMSO reductase, domains 1-3
1 54 SMART SM00926 Molybdop_Fe4S4_2
1 54 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
61 488 Pfam PF00384 Molybdopterin oxidoreductase
61 488 InterPro IPR006656 Molybdopterin oxidoreductase
616 643 ProSitePatterns PS00932 Prokaryotic molybdopterin oxidoreductases signature 3.
616 643 InterPro IPR006655 Molybdopterin oxidoreductase, prokaryotic, conserved site
435 452 ProSitePatterns PS00490 Prokaryotic molybdopterin oxidoreductases signature 2.
435 452 InterPro IPR006655 Molybdopterin oxidoreductase, prokaryotic, conserved site
140 334 Gene3D G3DSA:3.40.228.10 Dimethylsulfoxide Reductase, domain 2
1 55 FunFam G3DSA:2.20.25.90:FF:000001 Formate dehydrogenase subunit alpha
6 565 CDD cd02753 MopB_Formate-Dh-H
6 565 InterPro IPR041924 Formate dehydrogenase H, N-terminal
3 689 PANTHER PTHR43105 RESPIRATORY NITRATE REDUCTASE
7 686 NCBIfam TIGR01591 formate dehydrogenase subunit alpha
7 686 InterPro IPR006478 Formate dehydrogenase, alpha subunit
1 53 Pfam PF04879 Molybdopterin oxidoreductase Fe4S4 domain
1 53 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
572 688 CDD cd02790 MopB_CT_Formate-Dh_H
572 688 InterPro IPR041925 Formate dehydrogenase H, molybdopterin-binding domain
566 700 SUPERFAMILY SSF50692 ADC-like
566 700 InterPro IPR009010 Aspartate decarboxylase-like domain superfamily
1 56 ProSiteProfiles PS51669 Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
1 56 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S 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 #1
1.0
Likely same site as P2Rank 1 0.4 Å 55 shared residues 96% of smaller site
Unusual size
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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
0.988
Likely same site as FPocket 1 0.4 Å 55 shared residues 96% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.311
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Surrounding area
Site 3 P2Rank #3
0.112
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Surrounding area
Site 4 P2Rank #4
0.052
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Surrounding area
Site 5 P2Rank #5
0.018
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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_A0A0H3GR17
AlphaFold DB full sequence Viewing
ColabFold VK055_0372
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
2MD PDB via homolog 742.6 Da · LogP -2.53 · TPSA 346.6 Open detail RCSB PDB
4MO PDB via homolog Detail RCSB PDB
6MO PDB via homolog Detail RCSB PDB
FES PDB via homolog Detail RCSB PDB
H2S 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
2MD RCSB PDB P07658 742.6 Da LogP -2.53 TPSA 346.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…
4MO RCSB PDB P07658 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+4]
6MO RCSB PDB D5AQH0 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+6]
FES RCSB PDB D5AQH0 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
H2S RCSB PDB D5AQH0 34.1 Da LogP 0.11 TPSA 0.0 ✓ Ro5 ✓ Clean S
LCP RCSB PDB P81186 99.4 Da LogP -4.76 TPSA 92.2 ✓ Ro5 ✓ Clean [O-]Cl(=O)(=O)=O
MGD RCSB PDB P81186 740.6 Da LogP -2.06 TPSA 346.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…
MO RCSB PDB P81186 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo]
MOS RCSB PDB P39185 161.0 Da LogP 0.14 TPSA 34.1 ✓ Ro5 ✓ Clean O=[Mo](=O)S
NO2 RCSB PDB P07658 46.0 Da LogP 0.25 TPSA 52.5 ✓ Ro5 ✓ Clean N(=O)[O-]

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.