Protein target profile

KP13_32232

Formate dehydrogenase, nitrate-inducible, major subunit

Genome: KpKP13 Gene: AHE44401.1 fdnG 3D evidence: ColabFold model UniProt A0A844PNL7
Length 1025
Pocket druggability 0.928
Direct ligand evidence 0 62 total records
Functional annotation 0 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.

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
3.0% 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
Periplasmic

Structure confidence

ColabFold pLDDT
93.9 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

ColabFold / curated 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 0.928
Structure CB_KP13_32232
Pocket Pocket 1
P2Rank 0.951
Structure CB_KP13_32232
Pocket Pocket 1
ColabFold model
FPocket 0.928 · Pocket 1
P2Rank 0.951 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 144 / 4744 genomes with a hit
Prevalence 3.0%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MNQHPAWRNAMDVSRRKFFKICAGGMAGTTAAALGFAPKMALAQARNFKLLRAKEIRNTCTYCSVGCGLLMYSLGDGAKNAKEAIYHIEGDPDHPVSRGALCPKGAGLLDYVHSENRLRYPQYRAPGSDKWQRISWDEAFNRIARLMKADRDANFIEKNEQGVTVNRWLSTGMLCASAASNETGMLTQKFVRSLGMLAVDNQARVUHGPTVASLAPTFGRGAMTNHWVDIKNANVVVVMGGNAAEAHPVGFRWAMEAKNNNDATLIVVDPRFTRTASVADIYAPIRSGTDITFLSGVLLYLIENNKINAEYVKHYTNASLLVRDDFAFEEGLFSGYDAEKRQYDKSSWNYQFDENGYAKRDETLTHPRCVWNLLKQHVSRYTPEVVENICGTPKADFLKVCDVLASTSAADRTTTFLYALGWTQHTVGAQNIRTMAMIQLLLGNMGMAGGGVNALRGHSNIQGLTDLGLLSTSLPGYLTLPSDKQTDLQSYLSANTPKATLPEQVNYWSNYPKFFVSLMKSFYGEAAQKENDWGFEWLPKWDQAYDVIKYFNMMDNGNVTGYICQGFNPVASFPDKNKVVRSLSKLKYMVVIDPLVTETSTFWQNHGESNDVDPSAIQTEVFRLPSTCFAEEDGSIANSGRWLQWHWKGQDAPGEARNDGEILAGIYHRLRELYRTEGGKGAEPLLKMSWRYKQPDHPESEEVAKENNGYALADLYDQNGTLLAKKGQLLNSFALLRDDGSTASSCWIYTGSWTEQGNQMANRDNADPSGLGNTLGWAWAWPLNRRVLYNRASADINGKPWDAKRMLIQWNGNKWVGNDIPDFNTAPPGSNTGPFIMQQEGLGRLFALDKLAEGPFPEHYEPMETPLGTNPLHPKVVSSPVVRLYEEDAIRLGKKDKFPYVGTTYRLTEHFHTWTKHALLNSIAQPEQFVEISEGLAKSKGIANGDWVKVSSKRGFIRAVAVVTRRLRTLNVNGQQVETVGIPLHWGFEGVARKGYIANTLTPNVGDSNSQTPEYKAFLVNIEKA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

13 GO

Gene Ontology (GO)

13
  • GO:0047111 Catalysis of the reaction: ferricytochrome C-553 + formate = ferrocytochrome C-553 + CO2.
  • 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:0008863 Catalysis of the reaction: formate + NAD+ = CO2 + NADH.
  • 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:0045333 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).
  • 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:0009326 An enzyme complex that catalyzes the dehydrogenation of formate to produce carbon dioxide (CO2).
  • GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
  • GO:0036397 Catalysis of the reaction: formate + a quinone = CO2 + a quinol.
  • GO:0030151 Binding to a molybdenum ion (Mo).
  • GO:0009061 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
  • GO:0015944 The chemical reactions and pathways by which formate is converted to CO2.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

40 records
Show feature table
Start End DB Term Name
202 495 FunFam G3DSA:3.40.228.10:FF:000006 Formate dehydrogenase, alpha subunit, selenocysteine-containing
35 43 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
21 43 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
44 1025 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
54 114 Pfam PF04879 Molybdopterin oxidoreductase Fe4S4 domain
54 114 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
709 849 Gene3D G3DSA:3.40.228.10 Dimethylsulfoxide Reductase, domain 2
539 692 Gene3D G3DSA:3.40.50.740 -
1 43 ProSiteProfiles PS51318 Twin arginine translocation (Tat) signal profile.
1 43 InterPro IPR006311 Twin-arginine translocation pathway, signal sequence
45 169 FunFam G3DSA:3.30.200.210:FF:000003 Formate dehydrogenase-N subunit alpha
11 1025 PANTHER PTHR43598 TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE 2 SUBUNIT B
863 1025 SUPERFAMILY SSF50692 ADC-like
863 1025 InterPro IPR009010 Aspartate decarboxylase-like domain superfamily
850 1025 Gene3D G3DSA:2.40.40.20 -
21 34 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
903 1018 Pfam PF01568 Molydopterin dinucleotide binding domain
903 1018 InterPro IPR006657 Molybdopterin dinucleotide-binding domain
45 168 Gene3D G3DSA:3.30.200.210 -
527 692 FunFam G3DSA:3.40.50.740:FF:000007 Formate dehydrogenase, alpha subunit, selenocysteine-containing
117 599 Pfam PF00384 Molybdopterin oxidoreductase
117 599 InterPro IPR006656 Molybdopterin oxidoreductase
53 116 ProSiteProfiles PS51669 Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
53 116 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
1 20 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 43 Phobius SIGNAL_PEPTIDE Signal peptide region
896 1024 CDD cd02792 MopB_CT_Formate-Dh-Na-like
46 860 SUPERFAMILY SSF53706 Formate dehydrogenase/DMSO reductase, domains 1-3
53 114 SMART SM00926 Molybdop_Fe4S4_2
53 114 InterPro IPR006963 Molybdopterin oxidoreductase, 4Fe-4S domain
850 1025 FunFam G3DSA:2.40.40.20:FF:000017 Formate dehydrogenase, alpha subunit
202 492 Gene3D G3DSA:3.40.228.10 Dimethylsulfoxide Reductase, domain 2
57 883 CDD cd02752 MopB_Formate-Dh-Na-like
12 1024 NCBIfam TIGR01553 formate dehydrogenase-N subunit alpha
12 1024 InterPro IPR006443 Formate dehydrogenase-N, alpha subunit
701 849 FunFam G3DSA:3.40.228.10:FF:000011 Formate dehydrogenase-N subunit alpha
937 964 ProSitePatterns PS00932 Prokaryotic molybdopterin oxidoreductases signature 3.
937 964 InterPro IPR006655 Molybdopterin oxidoreductase, prokaryotic, conserved site
58 76 ProSitePatterns PS00551 Prokaryotic molybdopterin oxidoreductases signature 1.
58 76 InterPro IPR027467 Molybdopterin oxidoreductase, molybdopterin cofactor binding site

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
0.928
Likely same site as P2Rank 3 0.6 Å 20 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #23
0.358
Likely same site as P2Rank 2 4.1 Å 21 shared residues 84% of smaller site
Unusual size
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Surrounding area
Site 3 FPocket #2
0.214
Likely same site as P2Rank 1 5.5 Å 20 shared residues 95% of smaller site
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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
0.951
Likely same site as FPocket 2 5.5 Å 20 shared residues 95% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.876
Likely same site as FPocket 23 4.1 Å 21 shared residues 84% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.82
Likely same site as FPocket 1 0.6 Å 20 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.256
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Surrounding area
Site 5 P2Rank #5
0.109
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Surrounding area
All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 1

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
ColabFold KP13_32232
ColabFold full sequence Viewing

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.

62 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 12 records from similar proteins
Structural ligands 12 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
CDL PDB via homolog Detail RCSB PDB
FES 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 Q934F5 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 P24183 95.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Mo+6]
CDL RCSB PDB P24183 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
FES RCSB PDB D5AQH0 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
H2S RCSB PDB Q72EJ1 34.1 Da LogP 0.11 TPSA 0.0 ✓ Ro5 ✓ Clean S
HQO RCSB PDB P24183 259.3 Da LogP 3.69 TPSA 47.2 ✓ Ro5 Alert CCCCCCCc1cc(c2ccccc2[n+]1[O-])O
LCP RCSB PDB P81186 99.4 Da LogP -4.76 TPSA 92.2 ✓ Ro5 ✓ Clean [O-]Cl(=O)(=O)=O
MGD RCSB PDB P24183 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]
NO2 RCSB PDB P81186 46.0 Da LogP 0.25 TPSA 52.5 ✓ Ro5 ✓ Clean N(=O)[O-]
W RCSB PDB Q72EJ1 183.8 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [W+6]

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.