KpKP13 Protein target profile

protein rutD

Accession: KP13_03916

Gene: rutD AHE45338.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0AAW3FT13

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Length 267

Pocket druggability (P2Rank · AlphaFold DB model) 0.94

Direct ligand evidence 0 55 total records

Functional annotation 0 EC 2 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 0.94. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 5 structural and 0 bioactivity records.

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%): 28.431 Lower values reduce human off-target concern.
Human E-value: 4.27e-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 (%): 0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 96.56 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) 0.94

Structure A0AAW3FT13

Pocket Pocket 1

Druggability (FPocket) 0.27

Structure A0AAW3FT13

Pocket Pocket 2

ColabFold model

P2Rank 0.942 · Pocket 1

FPocket 0.708 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 39 / 4744 genomes with a hit

Prevalence 0.8%

Sequence

Primary amino-acid sequence viewer.

MMRLNIAPAPWPGAPVVVLSAGLGGGGGYWLAQRAALEEQYQLVSYDHNGTGENAGPLPADYSLATMAGELFSALQAAGIARFALVGHALGALIGLQLALDRPEAVSALALVNGWLSLSPHTRRCFQVRERLLHAGGAQAWVEAQPLFLYPAEWMAARLPRLEAEDALAISHFQGKENLLKRLQALKQADFSRRAAAIACPTLIISAADDLLVPASCSRVLQTAIPGSQLVEMPWGGHACNVTDADTFNTILRDGLSAMLPVARETR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization: Unknown

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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
99	112	PRINTS	PR00111	Alpha/beta hydrolase fold signature
99	112	InterPro	IPR000073	Alpha/beta hydrolase fold-1
202	216	PRINTS	PR00111	Alpha/beta hydrolase fold signature
202	216	InterPro	IPR000073	Alpha/beta hydrolase fold-1
85	98	PRINTS	PR00111	Alpha/beta hydrolase fold signature
85	98	InterPro	IPR000073	Alpha/beta hydrolase fold-1
40	55	PRINTS	PR00111	Alpha/beta hydrolase fold signature
40	55	InterPro	IPR000073	Alpha/beta hydrolase fold-1
1	259	Gene3D	G3DSA:3.40.50.1820	alpha/beta hydrolase
1	259	InterPro	IPR029058	Alpha/Beta hydrolase fold
14	256	PANTHER	PTHR43433	HYDROLASE, ALPHA/BETA FOLD FAMILY PROTEIN
2	258	NCBIfam	TIGR03611	pyrimidine utilization protein D
2	258	InterPro	IPR019913	Pyrimidine utilisation protein RutD
2	259	Hamap	MF_00832	Putative carbamate hydrolase RutD [rutD].
2	259	InterPro	IPR019913	Pyrimidine utilisation protein RutD
15	240	Pfam	PF00561	alpha/beta hydrolase fold
15	240	InterPro	IPR000073	Alpha/beta hydrolase fold-1
10	254	SUPERFAMILY	SSF53474	alpha/beta-Hydrolases
10	254	InterPro	IPR029058	Alpha/Beta hydrolase fold

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

0.94

Likely same site as FPocket 2 3.8 Å 16 shared residues 89% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.033

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Surrounding area

Pocket 3 P2Rank #3

0.007

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Surrounding area

Pocket 4 P2Rank #4

0.004

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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

0.27

Likely same site as P2Rank 1 3.8 Å 16 shared residues 89% of smaller site

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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

0.708

Likely same site as P2Rank 1 3.2 Å 24 shared residues 92% of smaller site

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Surrounding area

Pocket 2 FPocket #4

0.415

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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_A0AAW3FT13	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_03916	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

KKN PDB via homolog 150.1 Da · LogP 1.65 · TPSA 43.4 Open detail RCSB PDB

MLA PDB via homolog Detail RCSB PDB

PMS PDB via homolog Detail RCSB PDB

SHF PDB via homolog Detail RCSB PDB

TAM 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
KKN RCSB PDB	4JYM	Q9SZU7	150.1 Da LogP 1.65 TPSA 43.4	✓ Ro5	✓ Clean	`CC1=C2C=COC=C2OC1=O`
MLA RCSB PDB	1WOM	O07015	104.1 Da LogP -0.45 TPSA 74.6	✓ Ro5	✓ Clean	`C(C(=O)O)C(=O)O`
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`
TAM RCSB PDB	4HRY	Q9SZU7	163.2 Da LogP -1.17 TPSA 86.7	✓ Ro5	✓ Clean	`C(CO)C(CCO)(CCO)N`

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
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`
ZINC389634 ZINC	0.714	246.3 Da LogP 2.80 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)Cc1ccccc1`
ZINC14619253 ZINC	0.632	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCC(=O)O`
ZINC1841307 ZINC	0.632	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCC(=O)O`
ZINC1845839 ZINC	0.632	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCC(=O)O`
ZINC33822328 ZINC	0.632	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCCCC(=O)O`
ZINC5855130 ZINC	0.632	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCC(=O)O`
ZINC2575038 ZINC	0.625	205.3 Da LogP 0.00 TPSA 86.7	✓ Ro5	✓ Clean	`NC(CCCO)(CCCO)CCCO`
ZINC34080186 ZINC	0.609	266.3 Da LogP 0.46 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(O)Cc1ccccc1CS(=O)(=O)O`
ZINC32210235 ZINC	0.600	251.1 Da LogP 1.84 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(O)Cc1ccc(Br)cc1`
ZINC1679108 ZINC	0.583	324.4 Da LogP 2.17 TPSA 68.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)CS(=O)(=O)Cc1ccccc1`
ZINC163130 ZINC	0.560	232.3 Da LogP 2.66 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)c1ccccc1`
ZINC196676626 ZINC	0.560	340.4 Da LogP 1.14 TPSA 92.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)NNS(=O)(=O)Cc1ccccc1`
ZINC399776 ZINC	0.560	336.4 Da LogP 2.69 TPSA 68.3	✓ Ro5	✓ Clean	`O=S(=O)(/C=C/S(=O)(=O)Cc1ccccc1)Cc1ccccc1`
ZINC145170179 ZINC	0.556	250.3 Da LogP 0.48 TPSA 88.5	✓ Ro5	✓ Clean	`CS(=O)(=O)c1ccc(CS(=O)(=O)O)cc1`
ZINC1713408 ZINC	0.556	214.2 Da LogP 0.69 TPSA 71.4	✓ Ro5	✓ Clean	`O=C(O)CS(=O)(=O)Cc1ccccc1`
ZINC255190110 ZINC	0.556	386.5 Da LogP 3.63 TPSA 68.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)c1cccc(S(=O)(=O)Cc2ccccc2)c1`
ZINC26478554 ZINC	0.556	200.3 Da LogP 0.59 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(CCO)Cc1ccccc1`
ZINC35058157 ZINC	0.552	261.3 Da LogP 2.38 TPSA 60.2	✓ Ro5	✓ Clean	`Nc1cccc(CS(=O)(=O)Cc2ccccc2)c1`
ZINC14093286 ZINC	0.538	368.5 Da LogP 1.23 TPSA 92.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)NCCNS(=O)(=O)Cc1ccccc1`
ZINC147557095 ZINC	0.538	208.2 Da LogP 1.51 TPSA 69.7	✓ Ro5	✓ Clean	`CCOC(=O)c1c2ccocc-2oc1=O`
ZINC1163467 ZINC	0.536	436.6 Da LogP 4.79 TPSA 68.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)c1cccc2c(S(=O)(=O)Cc3ccccc3)c…`
ZINC32929750 ZINC	0.531	289.4 Da LogP 1.90 TPSA 77.2	✓ Ro5	✓ Clean	`NC(=O)c1cccc(CS(=O)(=O)Cc2ccccc2)c1`
ZINC143515753 ZINC	0.519	200.3 Da LogP 1.64 TPSA 54.4	✓ Ro5	✓ Clean	`CCc1ccccc1CS(=O)(=O)O`
ZINC29840 ZINC	0.519	261.3 Da LogP 2.31 TPSA 46.2	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)NCc1ccccc1`
ZINC45069273 ZINC	0.519	273.6 Da LogP 2.93 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)C(Cl)(Cl)Cl`
ZINC12805654 ZINC	0.517	444.6 Da LogP 2.93 TPSA 92.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)NCc1cccc(CNS(=O)(=O)Cc2ccccc2…`
ZINC13808031 ZINC	0.517	213.3 Da LogP -0.21 TPSA 98.5	✓ Ro5	✓ Clean	`NC(N)=NS(=O)(=O)Cc1ccccc1`
ZINC1561883 ZINC	0.517	229.3 Da LogP 0.19 TPSA 83.5	✓ Ro5	✓ Clean	`O=C(O)CNS(=O)(=O)Cc1ccccc1`
ZINC1641128 ZINC	0.517	242.3 Da LogP 2.68 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCCCc1ccccc1`
ZINC17021092 ZINC	0.517	228.3 Da LogP 1.07 TPSA 71.4	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)S(=O)(=O)Cc1ccccc1`
ZINC1704442 ZINC	0.517	228.3 Da LogP 1.07 TPSA 71.4	✓ Ro5	✓ Clean	`C[C@@H](C(=O)O)S(=O)(=O)Cc1ccccc1`
ZINC1764786 ZINC	0.517	217.2 Da LogP 0.98 TPSA 97.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(CS(=O)(=O)O)cc1`
ZINC3219150 ZINC	0.517	263.3 Da LogP 2.41 TPSA 57.6	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)N(O)c1ccccc1`
ZINC4512996 ZINC	0.517	228.3 Da LogP 1.08 TPSA 71.4	✓ Ro5	✓ Clean	`O=C(O)CCS(=O)(=O)Cc1ccccc1`
ZINC65593788 ZINC	0.517	274.4 Da LogP 3.42 TPSA 34.1	✓ Ro5	✓ Clean	`Cc1cc(C)cc(CS(=O)(=O)Cc2ccccc2)c1`
ZINC78978926 ZINC	0.516	266.7 Da LogP 3.31 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)c1cccc(Cl)c1`
ZINC96191894 ZINC	0.516	217.2 Da LogP 0.98 TPSA 97.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cccc(CS(=O)(=O)O)c1`
ZINC1566674 ZINC	0.500	400.5 Da LogP 3.92 TPSA 68.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)C(c1ccccc1)S(=O)(=O)Cc1ccccc1`
ZINC1682663 ZINC	0.500	202.2 Da LogP 0.44 TPSA 74.6	✓ Ro5	✓ Clean	`O=S(=O)(O)[C@H](O)Cc1ccccc1`
ZINC1926248 ZINC	0.500	416.5 Da LogP 3.57 TPSA 92.3	✓ Ro5	Alert	`O=S(=O)(Cc1ccccc1)Nc1ccc(NS(=O)(=O)Cc2ccccc2)cc1`
ZINC29837 ZINC	0.500	227.3 Da LogP 1.86 TPSA 37.4	✓ Ro5	✓ Clean	`CCN(CC)S(=O)(=O)Cc1ccccc1`
ZINC29852 ZINC	0.500	247.3 Da LogP 2.63 TPSA 46.2	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)Nc1ccccc1`
ZINC31723589 ZINC	0.500	226.3 Da LogP 1.20 TPSA 71.4	✓ Ro5	✓ Clean	`O=C(O)/C=C\S(=O)(=O)Cc1ccccc1`
ZINC399887 ZINC	0.500	274.3 Da LogP 2.48 TPSA 51.2	✓ Ro5	✓ Clean	`O=C(CS(=O)(=O)Cc1ccccc1)c1ccccc1`
ZINC40751845 ZINC	0.500	259.3 Da LogP -0.20 TPSA 77.8	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)N(CCO)CCO`
ZINC65593700 ZINC	0.500	314.3 Da LogP 3.82 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)Cc1cccc(C(F)(F)F)c1`
ZINC728426 ZINC	0.500	351.5 Da LogP 4.22 TPSA 37.4	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)N(Cc1ccccc1)Cc1ccccc1`
ZINC78758944 ZINC	0.500	315.2 Da LogP 4.11 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1cccc(Cl)c1)Cc1cccc(Cl)c1`
ZINC95630561 ZINC	0.500	248.3 Da LogP 2.52 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(Cc2ccccc2)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 A0AAW3FT13