KpATCC43816 Protein target profile

pyrimidine nucleotidase

Accession: VK055_2601

Gene: AIK81198.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GM80

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Length 225

Pocket druggability (P2Rank · AlphaFold DB model) 0.816

Direct ligand evidence 0 56 total records

Functional annotation 0 EC 1 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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 0.82. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 6 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 (%): 30.29 Lower values reduce human off-target concern.
Human E-value: 6.95e-16
Gut microbiome similarity: 2.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 31.429 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 96.29 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) 0.816

Structure A0A0H3GM80

Pocket Pocket 1

Druggability (FPocket) 0.23

Structure A0A0H3GM80

Pocket Pocket 8

ColabFold model

P2Rank 0.841 · Pocket 1

FPocket 0.603 · Pocket 2

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 96 / 4744 genomes with a hit

Prevalence 2.0%

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.

MKWDWIFFDADETLFTFDSFSGLQRMFLDYSVTFTAEDFQDYQAVNKPLWVDYQNGAITSLQLQHQRFDSWAERLNVPPGELNDAFMNAMAEICAPLPGAVSLLNALQGKVRMGIITNGFTSLQQTRLERTGLRDHFDLLIISEQVGVAKPDARIFDYALAQAGNPPRSRVLMVGDTAESDIRGGVNAGLATCWLNAHQRELPADLEPDWTVTSLSELEQLLCKH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0008253 Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
4	221	NCBIfam	TIGR02254	noncanonical pyrimidine nucleotidase, YjjG family
4	221	InterPro	IPR011951	HAD-superfamily hydrolase, subfamily IA, YjjG/PynA
98	189	NCBIfam	TIGR01549	HAD-IA family hydrolase
98	189	InterPro	IPR006439	HAD hydrolase, subfamily IA
1	223	PANTHER	PTHR47478	-
137	153	PRINTS	PR00413	Haloacid dehalogenase/epoxide hydrolase family signature
137	153	InterPro	IPR006439	HAD hydrolase, subfamily IA
106	119	PRINTS	PR00413	Haloacid dehalogenase/epoxide hydrolase family signature
106	119	InterPro	IPR006439	HAD hydrolase, subfamily IA
184	197	PRINTS	PR00413	Haloacid dehalogenase/epoxide hydrolase family signature
184	197	InterPro	IPR006439	HAD hydrolase, subfamily IA
80	194	Pfam	PF13419	Haloacid dehalogenase-like hydrolase
80	194	InterPro	IPR041492	Haloacid dehalogenase-like hydrolase
4	224	SFLD	SFLDG01135	C1.5.6: HAD, Beta-PGM, Phosphatase Like
4	224	SFLD	SFLDS00003	Haloacid Dehalogenase
97	196	CDD	cd04305	HAD_Neu5Ac-Pase_like
5	218	Gene3D	G3DSA:3.40.50.1000	-
5	218	InterPro	IPR023214	HAD superfamily
3	222	SUPERFAMILY	SSF56784	HAD-like
3	222	InterPro	IPR036412	HAD-like superfamily
16	95	Gene3D	G3DSA:1.10.150.240	Putative phosphatase; domain 2
16	95	InterPro	IPR023198	Phosphoglycolate phosphatase-like, domain 2
92	195	NCBIfam	TIGR01509	HAD-IA family hydrolase
92	195	InterPro	IPR006439	HAD hydrolase, subfamily IA

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

0.816

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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 #8

0.23

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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

0.603

Likely same site as P2Rank 1 2.4 Å 14 shared residues 93% of smaller site

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Surrounding area

Pocket 2 FPocket #12

0.241

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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_A0A0H3GM80	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_2601	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.

56 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 6 records from similar proteins

Structural ligands 6 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

AC0 PDB via homolog 120.2 Da · LogP 1.89 · TPSA 17.1 Open detail RCSB PDB

BUA PDB via homolog Detail RCSB PDB

LAC PDB via homolog Detail RCSB PDB

NHE PDB via homolog Detail RCSB PDB

TBU 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
AC0 RCSB PDB	6Q7N	O58216	120.2 Da LogP 1.89 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccccc1`
BUA RCSB PDB	1ZRM	Q53464	88.1 Da LogP 0.87 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC(=O)O`
LAC RCSB PDB	1QH9	Q53464	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)O`
NHE RCSB PDB	4YGR	B6YTD6	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=O)(=O)O`
TBU RCSB PDB	4YGQ	B6YTD6	74.1 Da LogP 0.78 TPSA 20.2	✓ Ro5	✓ Clean	`CC(C)(C)O`
VO4 RCSB PDB	4KNW	Q8TBE9	114.9 Da LogP -3.69 TPSA 86.2	✓ Ro5	✓ Clean	`[O-][V](=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
ZINC1710230 ZINC	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC3200262 ZINC	0.842	252.3 Da LogP 2.95 TPSA 51.2	✓ Ro5	Alert	`CC(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC36456728 ZINC	0.800	224.3 Da LogP 3.12 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC2004372 ZINC	0.786	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153 ZINC	0.786	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
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`
ZINC1039926 ZINC	0.625	220.3 Da LogP 3.29 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C#Cc2ccccc2)cc1`
ZINC143028 ZINC	0.625	228.3 Da LogP 4.04 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Sc2ccccc2)cc1`
ZINC1440490 ZINC	0.625	222.3 Da LogP 4.06 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(/C=C/c2ccccc2)cc1`
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(=…`
ZINC14981993 ZINC	0.625	224.3 Da LogP 3.12 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1cccc(C(=O)c2ccccc2)c1`
ZINC1562037 ZINC	0.625	210.3 Da LogP 3.48 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Cc2ccccc2)cc1`
ZINC1675948 ZINC	0.625	226.3 Da LogP 3.33 TPSA 41.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(NNc2ccccc2)cc1`
ZINC1845686 ZINC	0.625	224.3 Da LogP 3.67 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(CCc2ccccc2)cc1`
ZINC21999250 ZINC	0.625	211.3 Da LogP 3.63 TPSA 29.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Nc2ccccc2)cc1`
ZINC261810 ZINC	0.625	212.2 Da LogP 3.68 TPSA 26.3	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Oc2ccccc2)cc1`
ZINC4798948 ZINC	0.625	224.3 Da LogP 4.30 TPSA 41.8	✓ Ro5	Alert	`CC(=O)c1ccc(/N=N/c2ccccc2)cc1`
ZINC50452 ZINC	0.615	240.3 Da LogP 3.11 TPSA 43.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(OC(=O)c2ccccc2)cc1`
ZINC586797 ZINC	0.615	239.3 Da LogP 3.14 TPSA 46.2	✓ Ro5	✓ Clean	`CC(=O)c1ccc(NC(=O)c2ccccc2)cc1`
ZINC1672966 ZINC	0.611	210.2 Da LogP 2.75 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1)c1ccccc1`
ZINC1401590 ZINC	0.600	244.3 Da LogP 3.06 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([S@](=O)c2ccccc2)cc1`
ZINC143035 ZINC	0.600	260.3 Da LogP 2.72 TPSA 51.2	✓ Ro5	✓ Clean	`CC(=O)c1ccc(S(=O)(=O)c2ccccc2)cc1`
ZINC34354396 ZINC	0.600	224.3 Da LogP 4.04 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([C@@H](C)c2ccccc2)cc1`
ZINC34354398 ZINC	0.600	224.3 Da LogP 4.04 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([C@H](C)c2ccccc2)cc1`
ZINC4073660 ZINC	0.600	244.3 Da LogP 3.06 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([S@@](=O)c2ccccc2)cc1`
ZINC56557 ZINC	0.600	238.3 Da LogP 3.76 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(-c2ccc(C(C)=O)cc2)cc1`
ZINC336592 ZINC	0.583	224.3 Da LogP 3.12 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccccc1C(=O)c1ccccc1`
ZINC1529498 ZINC	0.579	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417 ZINC	0.579	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1577122 ZINC	0.579	208.3 Da LogP 4.64 TPSA 0.0	✓ Ro5	✓ Clean	`C/C(=C(/C)c1ccccc1)c1ccccc1`
ZINC1590838 ZINC	0.579	342.4 Da LogP 3.82 TPSA 68.3	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1)c1ccccc1`
ZINC16133932 ZINC	0.579	474.5 Da LogP 4.88 TPSA 102.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccc(C(=O)C(=O)c3cccc…`
ZINC1628119 ZINC	0.579	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC3123872 ZINC	0.579	208.3 Da LogP 4.64 TPSA 0.0	✓ Ro5	✓ Clean	`C/C(=C(\C)c1ccccc1)c1ccccc1`
ZINC117551598 ZINC	0.577	253.3 Da LogP 3.57 TPSA 37.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(N(C(C)=O)c2ccccc2)cc1`
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`
ZINC1556064 ZINC	0.577	252.4 Da LogP 4.45 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(CCCCc2ccccc2)cc1`
ZINC1621063 ZINC	0.577	268.3 Da LogP 2.82 TPSA 71.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C(=O)c2ccccc2C(=O)O)cc1`
ZINC1720928 ZINC	0.577	238.3 Da LogP 4.06 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(CCCc2ccccc2)cc1`
ZINC2039629 ZINC	0.577	222.3 Da LogP 4.06 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1cccc(/C=C/c2ccccc2)c1`
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`
ZINC47679 ZINC	0.577	254.3 Da LogP 3.53 TPSA 58.2	✓ Ro5	✓ Clean	`CC(=O)c1ccc(NC(=O)Nc2ccccc2)cc1`
ZINC1604259 ZINC	0.571	346.3 Da LogP 4.99 TPSA 51.2	✓ Ro5	✓ Clean	`O=C(c1ccccc1)P(C(=O)c1ccccc1)C(=O)c1ccccc1`
ZINC2113934064 ZINC	0.571	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCCCCCCC(=O)O`
ZINC2113934089 ZINC	0.571	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2378809 ZINC	0.571	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCC(=O)O`
ZINC5613445 ZINC	0.571	240.3 Da LogP 2.06 TPSA 38.0	✓ Ro5	✓ Clean	`CC(=O)c1cc[n+](CC(=O)c2ccccc2)cc1`

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 A0A0H3GM80