Protein target profile

VK055_5132

AMP nucleosidase

Genome: KpATCC43816 Gene: AIK83656.1 amn 3D evidence: Experimental + ColabFold model Metabolism 3 reactions UniProt W9BAW3

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Length 484

Pocket druggability 0.712

Metabolic reactions 3

Chokepoint No

Direct ligand evidence 0 32 total records

Functional annotation 1 EC 5 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. 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: No hit
Gut microbiome similarity: 2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 29.787 Higher values support similarity to known essential genes.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 92.66 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.712

Structure 7UWQ

Pocket Pocket 1

P2Rank 0.498

Structure 7UWQ

Pocket Pocket 1

ColabFold model

FPocket 0.591 · Pocket 3

P2Rank 0.699 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 113 / 4744 genomes with a hit

Prevalence 2.4%

Cross-references

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

Metabolic context

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

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome

Chokepoint Not a chokepoint

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MNIKAASLTPEQALAELEARYEASVTALRKAIGDYIDHNTLPDTEARAEGLFVYPQLSVSWDGADHKALKTRAWGRFTHAGCYTTTITNPKLFRNYLLEQLTLLYQDYGAHISVELSQHEIPYPYVIDGSTLTLDRSMSAGLTRYFPTTELSQIGDETADGLFHPTEFYPLSHFDARRVDFSLARLRHYTGTPAEHFQPYVLFTNYTRYVDEFVSWGCSQILDPDSPYIALSCAGGIWITAETEAPEQAISDLAWKKHQMPAWHLITHDGKGITLINIGVGPANAKTICDHLAVLRPDVWLMIGHCGGLRESQAIGDYVLAHAYLRDDHVLDAVLPPDIPIPSIAEVQRALYDATKQVSGMPGEEVKQRLRTGTVVTTDDRNWELRYSASALRFNLSRAVAIDMESATIAAQGYRFRVPYGTLLCVSDKPLHGEIKLPGQANRFYEGAISEHLQIGIRAIDLLRAEGDHMHSRKLRTFNEPPFR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

3.2.2.4

Gene Ontology (GO)

GO:0044209 The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0008714 Catalysis of the reaction: AMP + H2O = D-ribose 5-phosphate + adenine.
GO:0009116 The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
3	484	Hamap	MF_01932	AMP nucleosidase [amn].
3	484	InterPro	IPR011271	AMP nucleosidase
175	461	PANTHER	PTHR43691	URIDINE PHOSPHORYLASE
10	484	NCBIfam	TIGR01717	AMP nucleosidase
10	484	InterPro	IPR011271	AMP nucleosidase
9	484	SUPERFAMILY	SSF53167	Purine and uridine phosphorylases
9	484	InterPro	IPR035994	Nucleoside phosphorylase superfamily
12	167	Pfam	PF10423	Bacterial AMP nucleoside phosphorylase N-terminus
12	167	InterPro	IPR018953	AMP nucleoside phosphorylase, N-terminal
178	462	CDD	cd17762	AMN
178	462	InterPro	IPR047039	AMP nucleosidase, phosphorylase domain
173	484	Gene3D	G3DSA:3.40.50.1580	Nucleoside phosphorylase domain
173	484	InterPro	IPR035994	Nucleoside phosphorylase superfamily
173	484	FunFam	G3DSA:3.40.50.1580:FF:000005	AMP nucleosidase
266	431	Pfam	PF01048	Phosphorylase superfamily
266	431	InterPro	IPR000845	Nucleoside phosphorylase domain
1	172	Gene3D	G3DSA:3.30.1730.10	-
1	172	InterPro	IPR037109	AMP nucleoside phosphorylase, N-terminal domain superfamily

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

0.712

Likely same site as P2Rank 1 2.0 Å 14 shared residues 93% of smaller site

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.498

Likely same site as FPocket 1 2.0 Å 14 shared residues 93% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.365

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Surrounding area

Site 3 P2Rank #3

0.066

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Surrounding area

Site 4 P2Rank #4

0.056

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.699

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Surrounding area

Site 2 P2Rank #2

0.35

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Surrounding area

Site 3 P2Rank #3

0.288

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Surrounding area

Site 4 P2Rank #4

0.207

Likely same site as FPocket 3 0.5 Å 12 shared residues 92% of smaller site

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Surrounding area

Site 5 P2Rank #5

0.148

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Surrounding area

All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 7UWQ	X-ray	—	A	—	PDBe RCSB PDBj File	Viewing
ColabFold VK055_5132	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.

32 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 31 similarity-based ZINC candidates

Best available ligand signal

FMP PDB via homolog 347.2 Da · LogP -1.79 · TPSA 196.9 Open detail RCSB PDB

ZINC32138281 ZINC proposed compound · Tanimoto 0.590 Detail ZINC

ZINC8577182 ZINC proposed compound · Tanimoto 0.536 Detail ZINC

ZINC4972228 ZINC proposed compound · Tanimoto 0.534 Detail ZINC

ZINC8628081 ZINC proposed compound · Tanimoto 0.525 Detail ZINC

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
FMP RCSB PDB	1T8S	P0AE12	347.2 Da LogP -1.79 TPSA 196.9	1 viol.	✓ Clean	`c1nc2c(c(n1)N)[nH]nc2[C@H]3[C@@H]([C@@H]([C@H](…`

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
ZINC32138281 ZINC	0.590	384.4 Da LogP -1.37 TPSA 193.5	1 viol.	✓ Clean	`Nc1ncnc2c([C@@H]3O[C@H](CSCC[C@H](N)C(=O)O)[C@@…`
ZINC8577182 ZINC	0.536	268.2 Da LogP -1.79 TPSA 144.6	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](c2n[nH]c3c(O)ncnc23)[C@H](O)[C@…`
ZINC4972228 ZINC	0.534	310.3 Da LogP -1.30 TPSA 124.4	✓ Ro5	✓ Clean	`C[N+](C)(C)c1ncnc2c([C@H]3O[C@@H](CO)[C@@H](O)[…`
ZINC8628081 ZINC	0.525	282.3 Da LogP -2.21 TPSA 162.4	1 viol.	✓ Clean	`NNc1ncnc2c([C@H]3O[C@@H](CO)[C@@H](O)[C@H]3O)n[…`
ZINC8628082 ZINC	0.525	282.3 Da LogP -2.21 TPSA 162.4	1 viol.	✓ Clean	`NNc1ncnc2c([C@@H]3O[C@@H](CO)[C@@H](O)[C@H]3O)n…`
ZINC13518964 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167 ZINC	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8638190 ZINC	0.508	283.2 Da LogP -1.69 TPSA 156.6	1 viol.	✓ Clean	`OC[C@@H]1O[C@H](c2n[nH]c3c(NO)ncnc23)[C@H](O)[C…`
ZINC8638192 ZINC	0.508	283.2 Da LogP -1.69 TPSA 156.6	1 viol.	✓ Clean	`OC[C@@H]1O[C@@H](c2n[nH]c3c(NO)ncnc23)[C@H](O)[…`
ZINC8638194 ZINC	0.508	283.2 Da LogP -1.69 TPSA 156.6	1 viol.	✓ Clean	`OC[C@@H]1O[C@H](c2n[nH]c3c(NO)ncnc23)[C@@H](O)[…`
ZINC8638195 ZINC	0.508	283.2 Da LogP -1.69 TPSA 156.6	1 viol.	✓ Clean	`OC[C@@H]1O[C@@H](c2n[nH]c3c(NO)ncnc23)[C@@H](O)…`
ZINC4830848 ZINC	0.500	283.2 Da LogP -2.67 TPSA 164.5	✓ Ro5	✓ Clean	`Nc1c2[nH]nc([C@H]3O[C@@H](CO)[C@@H](O)[C@H]3O)c…`
ZINC4830849 ZINC	0.500	283.2 Da LogP -2.67 TPSA 164.5	✓ Ro5	✓ Clean	`Nc1c2[nH]nc([C@@H]3O[C@@H](CO)[C@@H](O)[C@H]3O)…`
ZINC4830850 ZINC	0.500	283.2 Da LogP -2.67 TPSA 164.5	✓ Ro5	✓ Clean	`Nc1c2[nH]nc([C@H]3O[C@@H](CO)[C@@H](O)[C@@H]3O)…`
ZINC4830852 ZINC	0.500	283.2 Da LogP -2.67 TPSA 164.5	✓ Ro5	✓ Clean	`Nc1c2[nH]nc([C@@H]3O[C@@H](CO)[C@@H](O)[C@@H]3O…`
ZINC5424976 ZINC	0.500	298.3 Da LogP -0.77 TPSA 124.4	✓ Ro5	✓ Clean	`CSc1ncnc2c([C@@H]3O[C@@H](CO)[C@@H](O)[C@@H]3O)…`
ZINC8659460 ZINC	0.500	324.2 Da LogP -2.83 TPSA 201.1	1 viol.	✓ Clean	`NC(=O)c1n[nH]c([C@@H]2O[C@H](COP(=O)(O)O)[C@H](…`
ZINC8659461 ZINC	0.500	324.2 Da LogP -2.83 TPSA 201.1	1 viol.	✓ Clean	`NC(=O)c1n[nH]c([C@@H]2O[C@@H](COP(=O)(O)O)[C@H]…`
ZINC8659462 ZINC	0.500	324.2 Da LogP -2.83 TPSA 201.1	1 viol.	✓ Clean	`NC(=O)c1n[nH]c([C@@H]2O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC8659463 ZINC	0.500	324.2 Da LogP -2.83 TPSA 201.1	1 viol.	✓ Clean	`NC(=O)c1n[nH]c([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H…`

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.

VK055_5132

Strong target candidate with converging metabolic, structural and chemical evidence.

Main supporting evidence

Risks to review

Evidence coverage

Prioritization evidence

Off-target risk

Essentiality

Localization

Structure confidence

Binding-site evidence

Cross-references

Sequence

Structure

Pathways

Metabolic context

Sequence

Functional annotations

Enzyme Commission (EC)

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · FPocket

Binding pockets · P2Rank

Binding pockets · FPocket

Binding pockets · P2Rank

Structural evidence

Ligand evidence