Protein target profile

VK055_4546

2OG-Fe(II) oxygenase superfamily protein

Genome: KpATCC43816 Gene: AIK83084.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A169ZP24
Length 355
Pocket druggability 0.991
Direct ligand evidence 0 82 total records
Functional annotation 1 EC 2 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
0.2% 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
Cytoplasmic

Structure confidence

ColabFold pLDDT
89.1 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 0.991
Structure A0A169ZP24
Pocket Pocket 1
P2Rank 0.973
Structure A0A169ZP24
Pocket Pocket 1
ColabFold model
FPocket 0.998 · Pocket 1
P2Rank 0.968 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 11 / 4744 genomes with a hit
Prevalence 0.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MTAVKHAFTELPTIDIRDLAGDDLARRQAVADAIGRAAREVGFFYITGHGIDPALIAGVREAAKQIFALPMEEKMNYYIGHSKSHKGYVPEGEEIYGSGKPDHKEAFDIGFQAADDHPLVLAGTPLIGANEWPDLPDFRARVLAYYDAVFALGHRLFDAFALALGLPEGYFKPMVTCPPAKLRLIHYPFDASVEDVPGIGAHTDYECFTLLLADQPGLEVLNEESVWIDAPPVKNAAGEEAFVINIGDMLEVLSAGTFVATAHRVRKVPQERYSFPLFFACDYHTLIRPLPTFLAAGEAGEYQELSIGEHMWSQALQTYRYLREKVNRGELQLPERARGTNTFGHLKKQAQQKNP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

2
  • GO:0102276 Catalysis of the reaction: 2-oxoglutarate(2-) + O2 + 2 H+ = ethene + 3 carbon dioxide + H2O.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
178 281 ProSiteProfiles PS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.
178 281 InterPro IPR005123 Oxoglutarate/iron-dependent dioxygenase
182 279 Pfam PF03171 2OG-Fe(II) oxygenase superfamily
182 279 InterPro IPR044861 Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain
8 321 SUPERFAMILY SSF51197 Clavaminate synthase-like
9 303 PANTHER PTHR10209 OXIDOREDUCTASE, 2OG-FE II OXYGENASE FAMILY PROTEIN
34 51 PRINTS PR00682 Isopenicillin N synthase signature
269 287 PRINTS PR00682 Isopenicillin N synthase signature
155 171 PRINTS PR00682 Isopenicillin N synthase signature
242 268 PRINTS PR00682 Isopenicillin N synthase signature
1 325 Gene3D G3DSA:2.60.120.330 -
1 325 InterPro IPR027443 Isopenicillin N synthase-like superfamily
11 134 Pfam PF14226 non-haem dioxygenase in morphine synthesis N-terminal
11 134 InterPro IPR026992 Non-haem dioxygenase N-terminal 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
0.991
Likely same site as P2Rank 1 1.6 Å 30 shared residues 97% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #6
0.436
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.973
Likely same site as FPocket 1 1.6 Å 30 shared residues 97% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.055
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.032
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_A0A169ZP24
AlphaFold DB full sequence Viewing
ColabFold VK055_4546
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.

82 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 32 records from similar proteins
Structural ligands 32 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ACC PDB via homolog 382.5 Da · LogP -1.80 · TPSA 160.4 Open detail RCSB PDB
ACV PDB via homolog Detail RCSB PDB
ACW PDB via homolog Detail RCSB PDB
AKG PDB via homolog Detail RCSB PDB
ASV 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
ACC RCSB PDB P05326 382.5 Da LogP -1.80 TPSA 160.4 1 viol. ✓ Clean CSC[C@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C@@H](…
ACV RCSB PDB P05326 363.4 Da LogP -0.79 TPSA 158.8 1 viol. ✓ Clean CC(C)[C@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C@@H…
ACW RCSB PDB P05326 375.4 Da LogP -0.65 TPSA 158.8 1 viol. ✓ Clean CC1(CC1)[C@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C…
AKG RCSB PDB Q96323 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
ASV RCSB PDB P05326 347.4 Da LogP -1.26 TPSA 158.8 1 viol. ✓ Clean C=C[C@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C@@H](…
BCV RCSB PDB P05326 361.4 Da LogP -1.04 TPSA 158.8 1 viol. ✓ Clean C1CC1[C@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C@@H…
DH2 RCSB PDB Q96323 304.3 Da LogP 1.19 TPSA 127.5 ✓ Ro5 Alert c1cc(c(cc1[C@H]2[C@@H](C(=O)c3c(cc(cc3O2)O)O)O)…
DQH RCSB PDB Q96323 304.3 Da LogP 1.19 TPSA 127.5 ✓ Ro5 Alert c1cc(c(cc1[C@@H]2[C@H](C(=O)c3c(cc(cc3O2)O)O)O)…
FYU RCSB PDB Q7RYZ9 140.1 Da LogP -1.12 TPSA 82.8 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1)C=O
HCV RCSB PDB P05326 377.5 Da LogP -0.40 TPSA 158.8 1 viol. ✓ Clean CC(C)[C@H](C(=O)O)NC(=O)[C@H](CCS)NC(=O)CCC[C@@…
HMU RCSB PDB Q7RYZ9 142.1 Da LogP -1.44 TPSA 86.0 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1)CO
HYO RCSB PDB Q6EZB3 289.4 Da LogP 1.93 TPSA 49.8 ✓ Ro5 ✓ Clean CN1[C@@H]2CC[C@H]1CC(C2)OC(=O)[C@H](CO)c3ccccc3
IP1 RCSB PDB P05326 359.4 Da LogP -0.80 TPSA 150.0 ✓ Ro5 ✓ Clean CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)CCC[C@@…
KKA RCSB PDB P05326 278.3 Da LogP -0.54 TPSA 129.7 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)N)CC(=O)N[C@@H](CCS)C(=O)O
M11 RCSB PDB P05326 378.4 Da LogP 0.02 TPSA 156.0 ✓ Ro5 ✓ Clean CC(C)[C@H](C(=O)O)OC(=O)[C@H]([C@H](C)S)NC(=O)C…
M2W RCSB PDB P05326 379.4 Da LogP -1.41 TPSA 168.0 1 viol. ✓ Clean C[C@@H]([C@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C…
M8F RCSB PDB P05326 395.5 Da LogP -0.69 TPSA 158.8 1 viol. ✓ Clean CSCC[C@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C@@H]…
M9F RCSB PDB P05326 395.5 Da LogP -0.70 TPSA 158.8 1 viol. ✓ Clean CC([C@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C@@H](…
NAR RCSB PDB Q96323 272.3 Da LogP 2.51 TPSA 87.0 ✓ Ro5 ✓ Clean c1cc(ccc1[C@@H]2CC(=O)c3c(cc(cc3O2)O)O)O
OGA RCSB PDB Q6EZB3 147.1 Da LogP -1.73 TPSA 103.7 ✓ Ro5 ✓ Clean C(C(=O)O)NC(=O)C(=O)O
OXY RCSB PDB P05326 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=O
QUE RCSB PDB Q96323 302.2 Da LogP 1.99 TPSA 131.4 ✓ Ro5 Alert c1cc(c(cc1C2=C(C(=O)c3c(cc(cc3O2)O)O)O)O)O
SIN RCSB PDB Q96323 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
TDR RCSB PDB Q7RYZ9 126.1 Da LogP -0.63 TPSA 65.7 ✓ Ro5 ✓ Clean CC1=CNC(=O)NC1=O
V10 RCSB PDB P05326 382.5 Da LogP -0.66 TPSA 156.0 ✓ Ro5 ✓ Clean CSC[C@@H](C(=O)O)OC(=O)[C@H](CS)NC(=O)CCC[C@@H]…
VB1 RCSB PDB P05326 349.4 Da LogP -1.04 TPSA 158.8 1 viol. ✓ Clean CC[C@@H](C(=O)O)NC(=O)[C@H](CS)NC(=O)CCC[C@@H](…
VVO RCSB PDB P05326 66.9 Da LogP -0.12 TPSA 17.1 ✓ Ro5 ✓ Clean O=[V+2]
W2X RCSB PDB P05326 392.4 Da LogP -0.88 TPSA 176.2 1 viol. ✓ Clean C[C@H](CO)[C@H](C(=O)O)OC(=O)[C@H](C(=C)S)NC(=O…
W6X RCSB PDB P05326 112.1 Da LogP 1.14 TPSA 17.1 ✓ Ro5 ✓ Clean CC(=O)C(F)(F)F
W6Z RCSB PDB P05326 130.1 Da LogP 0.25 TPSA 40.5 ✓ Ro5 ✓ Clean CC(C(F)(F)F)(O)O
WT4 RCSB PDB P05326 395.5 Da LogP -0.69 TPSA 158.8 1 viol. ✓ Clean CSC[C@H](C(=O)O)NC(=O)[C@H](CCS)NC(=O)CCC[C@@H]…
YT3 RCSB PDB B8M9K5 88.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Y+3]

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.