KpATCC43816 Protein target profile

pyrimidine utilization protein D

Accession: VK055_1442

Gene: rutD AIK80063.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A377TPP8

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Length 266

Pocket druggability (P2Rank · AlphaFold DB model) 0.939

Direct ligand evidence 0 55 total records

Functional annotation 1 EC 4 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

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.94, FPocket 0.87). Use the 3D pocket comparison to verify whether they identify the same site. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.87. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. Review the complete evidence below

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 (%): 28.431 Lower values reduce human off-target concern.
Human E-value: 3.97e-06
Gut microbiome similarity: 0.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 26.562 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 96.76 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) 0.939

Structure A0A377TPP8

Pocket Pocket 1

Druggability (FPocket) 0.872

Structure A0A377TPP8

Pocket Pocket 1

ColabFold model

P2Rank 0.948 · Pocket 1

FPocket 0.836 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 39 / 4744 genomes with a hit

Prevalence 0.8%

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.

MRLNIAPAPWPGAPVVVLSAGLGGGGGYWLAQRAALEEQYQLVSYDHNGTGENAGPLPADYSLATMAGELFSALQAAGIARFALVGHALGALIGLQLALDRPEAVSALALVNGWLSLSPHTRRCFQVRERLLHAGGAQAWVEAQPLFLYPAEWMAARLPRLEAEDALAISHFQGKENLLKRLQALKQADFSRRASAIACPTLIISAADDLLVPASCSRVLQTAIPGSQLVEMPRGGHACNVTDADTFNTILRDGLSAMLPVARETR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization: Unknown

Enzyme Commission (EC)

3.5.1.-

Gene Ontology (GO)

GO:0006212 The chemical reactions and pathways resulting in the breakdown of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA.
GO:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
GO:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
GO:0019740 A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary nitrogen source, usually ammonia, and then activates genes to scavenge the last traces of the primary nitrogen source and to transport and metabolize alternative nitrogen sources. The utilization process begins when the cell or organism detects nitrogen levels, includes the activation of genes whose products detect, transport or metabolize nitrogen-containing substances, and ends when nitrogen is incorporated into the cell or organism's metabolism.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
14	119	Pfam	PF00561	alpha/beta hydrolase fold
14	119	InterPro	IPR000073	Alpha/beta hydrolase fold-1
1	258	Gene3D	G3DSA:3.40.50.1820	alpha/beta hydrolase
1	258	InterPro	IPR029058	Alpha/Beta hydrolase fold
1	257	NCBIfam	TIGR03611	pyrimidine utilization protein D
1	257	InterPro	IPR019913	Pyrimidine utilisation protein RutD
98	111	PRINTS	PR00111	Alpha/beta hydrolase fold signature
98	111	InterPro	IPR000073	Alpha/beta hydrolase fold-1
84	97	PRINTS	PR00111	Alpha/beta hydrolase fold signature
84	97	InterPro	IPR000073	Alpha/beta hydrolase fold-1
39	54	PRINTS	PR00111	Alpha/beta hydrolase fold signature
39	54	InterPro	IPR000073	Alpha/beta hydrolase fold-1
201	215	PRINTS	PR00111	Alpha/beta hydrolase fold signature
201	215	InterPro	IPR000073	Alpha/beta hydrolase fold-1
9	253	SUPERFAMILY	SSF53474	alpha/beta-Hydrolases
9	253	InterPro	IPR029058	Alpha/Beta hydrolase fold
13	255	PANTHER	PTHR43433	HYDROLASE, ALPHA/BETA FOLD FAMILY PROTEIN
1	258	Hamap	MF_00832	Putative carbamate hydrolase RutD [rutD].
1	258	InterPro	IPR019913	Pyrimidine utilisation protein RutD

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

0.939

Likely same site as FPocket 1 2.5 Å 22 shared residues 96% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.032

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Surrounding area

Pocket 3 P2Rank #3

0.009

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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 #1

0.872

Likely same site as P2Rank 1 2.5 Å 22 shared residues 96% 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_A0A377TPP8	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_1442	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

MLA PDB via homolog 104.1 Da · LogP -0.45 · TPSA 74.6 Open detail RCSB PDB

PCS PDB via homolog Detail RCSB PDB

PHK PDB via homolog Detail RCSB PDB

PMS PDB via homolog Detail RCSB PDB

SHF 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
MLA RCSB PDB	1WOM	O07015	104.1 Da LogP -0.45 TPSA 74.6	✓ Ro5	✓ Clean	`C(C(=O)O)C(=O)O`
PCS RCSB PDB	1XQX	P96084	197.7 Da LogP 1.36 TPSA 43.1	✓ Ro5	✓ Clean	`c1ccc(cc1)C[C@@H](C(=O)CCl)N`
PHK RCSB PDB	1MU0	P96084	199.7 Da LogP 1.16 TPSA 46.2	✓ Ro5	✓ Clean	`c1ccc(cc1)C[C@@H]([C@H](CCl)O)N`
PMS RCSB PDB	1WPR	O07015	172.2 Da LogP 1.07 TPSA 54.4	✓ Ro5	✓ Clean	`c1ccc(cc1)CS(=O)(=O)O`
SHF RCSB PDB	2XUA	Q13KT2	116.1 Da LogP 0.44 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCC(=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
ZINC113264413 ZINC	0.778	317.4 Da LogP 3.98 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccc(-c3ccccc3)cc2)cc1)C(=O)O`
ZINC113264415 ZINC	0.778	317.4 Da LogP 3.98 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(-c2ccc(-c3ccccc3)cc2)cc1)C(=O)O`
ZINC2244337 ZINC	0.778	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccccc2)cc1)C(=O)O`
ZINC2244338 ZINC	0.778	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(-c2ccccc2)cc1)C(=O)O`
ZINC1764974 ZINC	0.750	266.3 Da LogP 0.46 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(O)Cc1ccc(CS(=O)(=O)O)cc1`
ZINC39351856 ZINC	0.731	328.4 Da LogP 1.26 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccc(C[C@H](N)C(=O)O)cc2)cc1)C…`
ZINC2561081 ZINC	0.724	269.3 Da LogP 1.87 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C(=O)c2ccccc2)cc1)C(=O)O`
ZINC2561082 ZINC	0.724	269.3 Da LogP 1.87 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C(=O)c2ccccc2)cc1)C(=O)O`
ZINC389634 ZINC	0.714	246.3 Da LogP 2.80 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)Cc1ccccc1`
ZINC113539705 ZINC	0.700	265.3 Da LogP 2.04 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C#Cc2ccccc2)cc1)C(=O)O`
ZINC113539708 ZINC	0.700	265.3 Da LogP 2.04 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C#Cc2ccccc2)cc1)C(=O)O`
ZINC116910786 ZINC	0.700	269.3 Da LogP 3.06 TPSA 88.0	✓ Ro5	Alert	`N[C@@H](Cc1ccc(/N=N/c2ccccc2)cc1)C(=O)O`
ZINC29566843 ZINC	0.700	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1cccc(-c2ccccc2)c1)C(=O)O`
ZINC29570997 ZINC	0.700	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(-c2ccccc2)c1)C(=O)O`
ZINC44283581 ZINC	0.700	257.3 Da LogP 2.43 TPSA 72.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(Oc2ccccc2)cc1)C(=O)O`
ZINC44283583 ZINC	0.700	257.3 Da LogP 2.43 TPSA 72.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(Oc2ccccc2)cc1)C(=O)O`
ZINC2111574 ZINC	0.692	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1C[C@H](N)C(=O)O)C(=O)O`
ZINC2111575 ZINC	0.692	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1C[C@@H](N)C(=O)O)C(=O)O`
ZINC2111578 ZINC	0.692	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1C[C@@H](N)C(=O)O)C(=O)O`
ZINC12648269 ZINC	0.690	237.3 Da LogP 0.73 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](C[C@@H](Cc1ccccc1)C(=O)O)C(=O)O`
ZINC5225893 ZINC	0.690	237.3 Da LogP 0.73 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](C[C@H](Cc1ccccc1)C(=O)O)C(=O)O`
ZINC133159 ZINC	0.688	271.3 Da LogP 2.22 TPSA 72.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(OCc2ccccc2)cc1)C(=O)O`
ZINC133162 ZINC	0.688	271.3 Da LogP 2.22 TPSA 72.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(OCc2ccccc2)cc1)C(=O)O`
ZINC32333 ZINC	0.679	244.1 Da LogP 1.40 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(Br)cc1)C(=O)O`
ZINC32334 ZINC	0.679	244.1 Da LogP 1.40 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(Br)cc1)C(=O)O`
ZINC3679925 ZINC	0.679	291.1 Da LogP 1.25 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(I)cc1)C(=O)O`
ZINC391104 ZINC	0.679	291.1 Da LogP 1.25 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(I)cc1)C(=O)O`
ZINC4202286 ZINC	0.679	209.2 Da LogP 0.34 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C(=O)O)cc1)C(=O)O`
ZINC4202287 ZINC	0.679	209.2 Da LogP 0.34 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C(=O)O)cc1)C(=O)O`
ZINC6092920 ZINC	0.679	223.2 Da LogP 0.27 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(CC(=O)O)cc1)C(=O)O`
ZINC6506146 ZINC	0.679	223.2 Da LogP 0.27 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(CC(=O)O)cc1)C(=O)O`
ZINC6580731 ZINC	0.679	225.3 Da LogP 2.44 TPSA 43.1	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1)C(=O)c1ccccc1`
ZINC90624143 ZINC	0.679	225.3 Da LogP 2.44 TPSA 43.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)C(=O)c1ccccc1`
ZINC21989078 ZINC	0.667	284.4 Da LogP 1.88 TPSA 72.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)C[C@H](O)[C@@H](N)Cc1ccccc1`
ZINC54918280 ZINC	0.667	254.3 Da LogP 1.87 TPSA 55.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)C(=O)NCc1ccccc1`
ZINC54918281 ZINC	0.667	254.3 Da LogP 1.87 TPSA 55.1	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1)C(=O)NCc1ccccc1`
ZINC14982778 ZINC	0.655	207.2 Da LogP 0.84 TPSA 80.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C[C@@H](N)C(=O)O)cc1`
ZINC14982780 ZINC	0.655	207.2 Da LogP 0.84 TPSA 80.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C[C@H](N)C(=O)O)cc1`
ZINC156948 ZINC	0.655	255.3 Da LogP 2.30 TPSA 52.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)C(=O)OCc1ccccc1`
ZINC2575618 ZINC	0.655	208.2 Da LogP -0.26 TPSA 106.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc(C[C@H](N)C(=O)O)cc1`
ZINC391855 ZINC	0.655	255.3 Da LogP 2.30 TPSA 52.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1)C(=O)OCc1ccccc1`
ZINC4241956 ZINC	0.655	208.2 Da LogP -0.26 TPSA 106.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc(C[C@@H](N)C(=O)O)cc1`
ZINC128259 ZINC	0.645	215.3 Da LogP 1.79 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc2ccccc2c1)C(=O)O`
ZINC1569732 ZINC	0.645	222.2 Da LogP -0.24 TPSA 92.4	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1)C(=O)NCC(=O)O`
ZINC1569733 ZINC	0.645	222.2 Da LogP -0.24 TPSA 92.4	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)C(=O)NCC(=O)O`
ZINC1667741 ZINC	0.645	209.2 Da LogP 0.34 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](Cc1cccc(C(=O)O)c1)C(=O)O`
ZINC2539998 ZINC	0.645	283.2 Da LogP -0.44 TPSA 147.2	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(OC(C(=O)O)C(=O)O)cc1)C(=O)O`
ZINC2557958 ZINC	0.645	209.2 Da LogP 0.34 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(C(=O)O)c1)C(=O)O`
ZINC3679860 ZINC	0.645	244.1 Da LogP 1.40 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(Br)c1)C(=O)O`
ZINC3679924 ZINC	0.645	291.1 Da LogP 1.25 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1cccc(I)c1)C(=O)O`

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 A0A377TPP8