KpATCC43816 Protein target profile

cupin superfamily protein

Accession: VK055_1328

Gene: AIK79951.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GVM4

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Length 373

Pocket druggability (P2Rank · AlphaFold DB model) 0.922

Direct ligand evidence 0 55 total records

Functional annotation 0 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.

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.92. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 5 structural and 0 bioactivity records.

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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 (%): 37.5 Lower values reduce human off-target concern.
Human E-value: 7.35e-07
Gut microbiome similarity: 2.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 87.062 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 96.83 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) 0.922

Structure A0A0H3GVM4

Pocket Pocket 1

Druggability (FPocket) 0.862

Structure A0A0H3GVM4

Pocket Pocket 2

ColabFold model

P2Rank 0.923 · Pocket 1

FPocket 0.621 · Pocket 2

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 118 / 4744 genomes with a hit

Prevalence 2.5%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MDYQLTLNWPDFIERYWQKRPVVLKRGFANFIDPISPDELAGLAMESEVDSRLVSHQDGKWQVSHGPFESYDHLSENNWSLLVQAVNHWHEPSAALMHPFRALPDWRIDDLMISFSVPGGGVGPHLDQYDVFIIQGTGRRRWRVGEKVPMKQHCPHPDLLQVDPFEAIIDEEMEPGDILYIPPGFPHEGYSLENSLNYSVGYRAPNARELFSGFADYVLQRELGSQRYADPDVPSRDHPADILPTELDRLREMMLGLINQPEHFKQWFGEFITQSRHELDVAPPEPPYQPDEIYDALQQGDTLERLGGLRVLRIDGEVFVNGEKINSPHRPALDALATHLTLRADHFGDALEDPSFLAMLAALVNSGYWFFGD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0016706 Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
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
2	204	FunFam	G3DSA:2.60.120.650:FF:000012	Cupin superfamily protein family
8	225	PANTHER	PTHR13096	MINA53 MYC INDUCED NUCLEAR ANTIGEN
8	225	InterPro	IPR039994	JmjC domain-containing
257	369	Pfam	PF20514	ROXA-like winged helix
257	369	InterPro	IPR046799	ROXA-like, winged helix
92	219	ProSiteProfiles	PS51184	JmjC domain profile.
92	219	InterPro	IPR003347	JmjC domain
2	204	Gene3D	G3DSA:2.60.120.650	Cupin
7	292	SUPERFAMILY	SSF51197	Clavaminate synthase-like
205	372	Gene3D	G3DSA:3.40.366.30	50S ribosomal protein L16 arginine hydroxylase; Chain A, Domain 2
92	215	SMART	SM00558	cupin_9
92	215	InterPro	IPR003347	JmjC domain
96	210	Pfam	PF08007	JmjC domain
96	210	InterPro	IPR003347	JmjC 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 · P2Rank

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

Pocket 1 P2Rank #1

0.922

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Surrounding area

Pocket 2 P2Rank #2

0.532

Likely same site as FPocket 2 2.7 Å 18 shared residues 95% of smaller site

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Surrounding area

Pocket 3 P2Rank #3

0.237

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Surrounding area

Pocket 4 P2Rank #4

0.236

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Surrounding area

Pocket 5 P2Rank #5

0.048

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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2

0.862 Unusual size

Likely same site as P2Rank 2 2.7 Å 18 shared residues 95% of smaller site

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Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.923

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Surrounding area

Pocket 2 P2Rank #2

0.55

Likely same site as FPocket 2 2.9 Å 16 shared residues 100% of smaller site

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Surrounding area

Pocket 3 P2Rank #3

0.147

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Surrounding area

Pocket 4 P2Rank #4

0.137

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Surrounding area

Pocket 5 P2Rank #5

0.045

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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_A0A0H3GVM4	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_1328	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.

55 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

AKG PDB via homolog 146.1 Da · LogP -0.50 · TPSA 91.7 Open detail RCSB PDB

OGA PDB via homolog Detail RCSB PDB

PD2 PDB via homolog Detail RCSB PDB

SIN PDB via homolog Detail RCSB PDB

UN9 PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
AKG RCSB PDB	4LIT	P27431	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
OGA RCSB PDB	4CUG	D0MK34	147.1 Da LogP -1.73 TPSA 103.7	✓ Ro5	✓ Clean	`C(C(=O)O)NC(=O)C(=O)O`
PD2 RCSB PDB	4DIQ	Q9H6W3	167.1 Da LogP 0.48 TPSA 87.5	✓ Ro5	✓ Clean	`c1cnc(cc1C(=O)O)C(=O)O`
SIN RCSB PDB	4LIV	P27431	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)O`
UN9 RCSB PDB	4CSW	D0MK34	280.7 Da LogP 1.41 TPSA 99.5	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(c(nc2Cl)C(=O)NCC(=O)O)O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC7670 ZINC	1.000	280.7 Da LogP 1.41 TPSA 99.5	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)c1nc(Cl)c2ccccc2c1O`
ZINC15782053 ZINC	0.690	227.2 Da LogP 2.01 TPSA 67.3	✓ Ro5	✓ Clean	`O=C(c1ccccc1)c1ccnc(C(=O)O)c1`
ZINC331417 ZINC	0.690	227.2 Da LogP 2.01 TPSA 67.3	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(C(=O)c2ccccc2)c1`
ZINC38880695 ZINC	0.680	244.2 Da LogP 1.54 TPSA 100.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccnc(C(=O)O)c2)ccn1`
ZINC56644 ZINC	0.680	244.2 Da LogP 1.54 TPSA 100.4	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2cc(C(=O)O)ccn2)c1`
ZINC35570360 ZINC	0.667	223.6 Da LogP 2.29 TPSA 70.4	✓ Ro5	✓ Clean	`O=C(O)c1nc(Cl)c2ccccc2c1O`
ZINC166201325 ZINC	0.656	223.2 Da LogP 1.74 TPSA 76.5	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)c1ccnc(C(=O)O)c1`
ZINC26439009 ZINC	0.655	243.2 Da LogP 2.15 TPSA 87.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccnc(C(=O)O)c2)cc1`
ZINC3593496 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC14686440 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC390821980 ZINC	0.625	223.2 Da LogP 1.74 TPSA 76.5	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)c1cc(C(=O)O)ccn1`
ZINC151256 ZINC	0.607	202.0 Da LogP 1.54 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1cc(Br)ccn1`
ZINC333016 ZINC	0.607	249.0 Da LogP 1.38 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1cc(I)ccn1`
ZINC3866429 ZINC	0.607	202.0 Da LogP 1.54 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(Br)c1`
ZINC4352682 ZINC	0.607	249.0 Da LogP 1.38 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(I)c1`
ZINC38342145 ZINC	0.600	237.6 Da LogP 2.38 TPSA 59.4	✓ Ro5	✓ Clean	`COC(=O)c1nc(Cl)c2ccccc2c1O`
ZINC35654093 ZINC	0.586	365.3 Da LogP 2.30 TPSA 150.6	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2cc(C(=O)O)cc(-c3cc(C(=O)O)ccn3)…`
ZINC47214440 ZINC	0.586	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccncc2)ccn1`
ZINC47214422 ZINC	0.581	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2ccncc2)c1`
ZINC13398039 ZINC	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012 ZINC	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC168888549 ZINC	0.571	284.3 Da LogP -0.35 TPSA 104.6	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)N2CCS(=O)(=O)CC2)ccn1`
ZINC2598993 ZINC	0.567	203.2 Da LogP 0.03 TPSA 104.6	✓ Ro5	✓ Clean	`O=C(O)c1cc(S(=O)(=O)O)ccn1`
ZINC146315135 ZINC	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336 ZINC	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC124644877 ZINC	0.553	264.3 Da LogP 0.81 TPSA 99.5	✓ Ro5	✓ Clean	`O=C(N[C@@H]1CCCC[C@@H]1O)c1ccnc(C(=O)O)c1`
ZINC124645116 ZINC	0.553	264.3 Da LogP 0.81 TPSA 99.5	✓ Ro5	✓ Clean	`O=C(N[C@H]1CCCC[C@@H]1O)c1ccnc(C(=O)O)c1`
ZINC124645281 ZINC	0.553	264.3 Da LogP 0.81 TPSA 99.5	✓ Ro5	✓ Clean	`O=C(N[C@@H]1CCCC[C@H]1O)c1ccnc(C(=O)O)c1`
ZINC124645494 ZINC	0.553	264.3 Da LogP 0.81 TPSA 99.5	✓ Ro5	✓ Clean	`O=C(N[C@H]1CCCC[C@H]1O)c1ccnc(C(=O)O)c1`
ZINC136976573 ZINC	0.553	250.3 Da LogP 0.69 TPSA 88.5	✓ Ro5	✓ Clean	`O=C(NC1CCOCC1)c1ccnc(C(=O)O)c1`
ZINC1708388 ZINC	0.548	287.3 Da LogP 3.54 TPSA 47.0	✓ Ro5	✓ Clean	`O=C(c1ccccc1)c1ccnc(C(=O)c2ccccc2)c1`
ZINC20357742 ZINC	0.548	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2ccccn2)c1`
ZINC2598999 ZINC	0.548	203.2 Da LogP 0.03 TPSA 104.6	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(S(=O)(=O)O)c1`
ZINC38283909 ZINC	0.548	214.2 Da LogP 2.15 TPSA 63.1	✓ Ro5	✓ Clean	`Cc1ccnc(-c2cc(C(=O)O)ccn2)c1`
ZINC65347060 ZINC	0.548	213.2 Da LogP 2.76 TPSA 50.2	✓ Ro5	✓ Clean	`Cc1ccc(-c2ccnc(C(=O)O)c2)cc1`
ZINC74941936 ZINC	0.548	304.3 Da LogP 1.33 TPSA 118.8	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(OCCOc2cc(C(=O)O)ccn2)c1`
ZINC98213921 ZINC	0.545	207.1 Da LogP 1.68 TPSA 59.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(OC(F)(F)F)ccn1`
ZINC263424469 ZINC	0.541	220.2 Da LogP 0.92 TPSA 79.3	✓ Ro5	✓ Clean	`C[C@@H]1C[C@H]1NC(=O)c1cc(C(=O)O)ccn1`
ZINC263424470 ZINC	0.541	220.2 Da LogP 0.92 TPSA 79.3	✓ Ro5	✓ Clean	`C[C@H]1C[C@H]1NC(=O)c1cc(C(=O)O)ccn1`
ZINC263424471 ZINC	0.541	220.2 Da LogP 0.92 TPSA 79.3	✓ Ro5	✓ Clean	`C[C@@H]1C[C@@H]1NC(=O)c1cc(C(=O)O)ccn1`
ZINC263424472 ZINC	0.541	220.2 Da LogP 0.92 TPSA 79.3	✓ Ro5	✓ Clean	`C[C@H]1C[C@@H]1NC(=O)c1cc(C(=O)O)ccn1`
ZINC71257465 ZINC	0.540	352.3 Da LogP 2.86 TPSA 108.8	✓ Ro5	✓ Clean	`Cc1nc(C(=O)NCC(=O)O)c(O)c2ccc(Oc3ccccc3)cc12`
ZINC1595538 ZINC	0.538	211.1 Da LogP 0.18 TPSA 124.8	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)nc(C(=O)O)c1`
ZINC306145916 ZINC	0.531	241.1 Da LogP 2.43 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(C(F)(F)C(F)(F)F)c1`
ZINC42684404 ZINC	0.531	201.2 Da LogP 0.18 TPSA 84.3	✓ Ro5	✓ Clean	`CS(=O)(=O)c1cc(C(=O)O)ccn1`
ZINC65348611 ZINC	0.531	268.1 Da LogP 3.75 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccc(Cl)c(Cl)c2)ccn1`
ZINC79006721 ZINC	0.531	202.2 Da LogP -0.57 TPSA 110.4	✓ Ro5	✓ Clean	`NS(=O)(=O)c1cc(C(=O)O)ccn1`

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.

Sequence

UniProt A0A0H3GVM4