KpATCC43816 Protein target profile

hydrogenase 3 and formate hydrogenlyase complex,HycG subunit

Accession: VK055_4458

Gene: AIK83001.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GWP2
Length 255
Pocket druggability (P2Rank · AlphaFold DB model) 0.232
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 61 total records
Functional annotation 0 EC 5 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 (%)
37.086 Lower values reduce human off-target concern.
Human E-value
9.65e-28
Gut microbiome similarity
10.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
94.99 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.232
Structure A0A0H3GWP2
Pocket Pocket 1
Druggability (FPocket) 0.429
Structure A0A0H3GWP2
Pocket Pocket 7
ColabFold model
P2Rank 0.096 · Pocket 1
FPocket 0.516 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 505 / 4744 genomes with a hit
Prevalence 10.6%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 88.3% of genes in this genome.

Relative network centrality 88.3% more central than 88.3% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

2 reactions 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.

MSTLLGPRDENGIPVPMTVDESIASMKASLLKKIKRSAYVYRVDCGGCNGCEIEIFATLSPLFDAERFGIKVVPSPRHADILLFTGAVTRAMRSPALRAWQSAPDPKICISYGACGNSGGIFHDLYCVWGGTDKIVPVDVYIPGCPPTPAATLYGFAMALGLLEQKIHARLPGELDEQPTELLHADMVQPLRVRIDREARRLAGYRYGRQIADDYMRLLGQGDSQVLRWLEAEKDPRLTEIVTHLNQVVEGARIR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

5
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • 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: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.
  • GO:0008137 Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) = NAD+ + ubiquinol + 4 H+(out).
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

7 records
Show feature table
Start End DB Term Name
18 180 Gene3D G3DSA:3.40.50.12280 -
4 174 PANTHER PTHR42989 HYDROGENASE-4 COMPONENT I
131 147 ProSitePatterns PS01150 Respiratory-chain NADH dehydrogenase 20 Kd subunit signature.
131 147 InterPro IPR006138 NADH-ubiquinone oxidoreductase, 20 Kd subunit
36 169 SUPERFAMILY SSF56770 HydA/Nqo6-like
48 157 Pfam PF01058 NADH ubiquinone oxidoreductase, 20 Kd subunit
48 157 InterPro IPR006137 NADH:ubiquinone oxidoreductase-like, 20kDa subunit

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.

Download VMD script Full viewer

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Drag to rotate — click the view, then scroll to zoom.

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.232
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.033
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.031
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.016
Likely same site as FPocket 12 2.1 Å 7 shared residues 100% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #7
0.429
Show in viewer
Surrounding area
Pocket 2 FPocket #12
0.283
Likely same site as P2Rank 4 2.1 Å 7 shared residues 100% 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_A0A0H3GWP2
AlphaFold DB full sequence Viewing
ColabFold VK055_4458
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.

61 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 10 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3PE PDB via homolog 748.1 Da · LogP 12.06 · TPSA 134.4 Open detail RCSB PDB
8Q1 PDB via homolog Detail RCSB PDB
CDL PDB via homolog Detail RCSB PDB
EHZ 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
3PE RCSB PDB W5PPP6 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
8Q1 RCSB PDB O75251 540.7 Da LogP 3.29 TPSA 162.3 1 viol. ✓ Clean CCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)…
CDL RCSB PDB Q9DC70 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
EHZ RCSB PDB Q9DC70 584.7 Da LogP 3.04 TPSA 182.5 2 viol. ✓ Clean CCCCCCCCCCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H]…
FES RCSB PDB A0A1S3U8J5 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
NFU RCSB PDB Q8U0Z8 195.6 Da LogP -0.25 TPSA 64.7 ✓ Ro5 ✓ Clean C(=O)[Fe](C#N)(C#N)[Ni]
PC1 RCSB PDB Q9DC70 790.2 Da LogP 12.17 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])…
PEE RCSB PDB O75251 744.0 Da LogP 11.61 TPSA 134.4 2 viol. ✓ Clean CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN…
PLX RCSB PDB O75251 767.1 Da LogP 11.61 TPSA 114.7 2 viol. ✓ Clean CCCCCCCCCCCCCCCCC[C@@H](O)O[C@H](CO[C@@H](CCCCC…
ZMP RCSB PDB W5PPP6 568.7 Da LogP 4.07 TPSA 162.3 1 viol. ✓ Clean CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(C…

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.

Cross-references

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