Protein target profile

KP13_15895

Agmatinase

Genome: KpKP13 Gene: ANJ86590.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A6A8ECW2

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Length 316

Pocket druggability 0.531

Direct ligand evidence 0 53 total records

Functional annotation 1 EC 5 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

Moderate predicted binding pocket FPocket selected-pocket score 0.53. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.59. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 3 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 (%): 61.364 Lower values reduce human off-target concern.
Human E-value: 5.34e-136
Gut microbiome similarity: 0.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 43.098 Higher values support similarity to known essential genes.
DEG E-value: 1.5199999999999999e-61 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 97.3 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.531

Structure A0A6A8ECW2

Pocket Pocket 3

P2Rank 0.592

Structure A0A6A8ECW2

Pocket Pocket 1

ColabFold model

FPocket 0.264 · Pocket 1

P2Rank 0.597 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 23 / 4744 genomes with a hit

Prevalence 0.5%

Cross-references

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

Sequence

UniProt A0A6A8ECW2

Sequence

Primary amino-acid sequence viewer.

MDNLFHQPQGGNEMPRFAGRATMMRLPFIEDLQGLDAAFVGIPLDIGTSQRSGTRYGPRYIRAESVMIRPYNMATGAAPFDSLSVADIGDVPINTYSLLKSVQIIEDYYTGLNSYPLIPLTLGGDHTITLPILRALTKKHGPVGLIHVDAHTDTNDEMFGEKIAHGTTFRRAVEEGLLDLKRVVQIGQRAQGYAAGDFQWGVDQGFRLVQAEQCWHTSLAPLMAEVRQQMGNGPVYLSFDIDSLDPIWAPGTGTPEVGGLTSIQALEIVRGCRGLNLIGADLVEVSPPYDVSGNTSQLAANMLYEMLCVLPGVKYA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

3.5.3.11

Gene Ontology (GO)

GO:0016813 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amidine, a compound of the form R-C(=NH)-NH2.
GO:0046872 Binding to a metal ion.
GO:0008783 Catalysis of the reaction: agmatine + H2O = putrescine + urea.
GO:0047971 Catalysis of the reaction: 4-guanidinobutanoate + H2O = 4-aminobutanoate + urea.
GO:0033389 The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from arginine via agmatine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
235	264	PRINTS	PR00116	Arginase signature
235	264	InterPro	IPR006035	Ureohydrolase
122	137	PRINTS	PR00116	Arginase signature
122	137	InterPro	IPR006035	Ureohydrolase
2	316	Gene3D	G3DSA:3.40.800.10	Ureohydrolase domain
36	308	NCBIfam	TIGR01230	agmatinase
36	308	InterPro	IPR005925	Agmatinase-related
14	313	PIRSF	PIRSF036979	Arginase
14	313	InterPro	IPR006035	Ureohydrolase
2	316	FunFam	G3DSA:3.40.800.10:FF:000002	Agmatinase
25	316	ProSiteProfiles	PS51409	Arginase family profile.
25	316	InterPro	IPR006035	Ureohydrolase
14	309	SUPERFAMILY	SSF52768	Arginase/deacetylase
14	309	InterPro	IPR023696	Ureohydrolase domain superfamily
36	307	Pfam	PF00491	Arginase family
36	307	InterPro	IPR006035	Ureohydrolase
19	307	CDD	cd11592	Agmatinase_PAH
238	259	ProSitePatterns	PS01053	Arginase family signature.
238	259	InterPro	IPR020855	Ureohydrolase, manganese-binding site
6	311	PANTHER	PTHR11358	ARGINASE/AGMATINASE
6	311	InterPro	IPR006035	Ureohydrolase

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 #3

0.531

Likely same site as P2Rank 1 3.0 Å 15 shared residues 83% of smaller site

Unusual size

Show in viewer

Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.592

Likely same site as FPocket 3 3.0 Å 15 shared residues 83% 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_A0A6A8ECW2	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_15895	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.

53 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

16D PDB via homolog 116.2 Da · LogP 0.46 · TPSA 52.0 Open detail RCSB PDB

CAC PDB via homolog Detail RCSB PDB

ORN PDB via homolog Detail RCSB PDB

ZINC1685531 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC34273707 ZINC proposed compound · Tanimoto 1.000 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
16D RCSB PDB	3NIP	Q9I6K2	116.2 Da LogP 0.46 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCCN)CCN`
CAC RCSB PDB	3M1R	P42068	137.0 Da LogP -0.52 TPSA 40.1	✓ Ro5	✓ Clean	`C[As](=O)(C)[O-]`
ORN RCSB PDB	6VST	G7JFU5	132.2 Da LogP -0.86 TPSA 89.3	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)N)CN`

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
ZINC1685531 ZINC	1.000	200.4 Da LogP 2.80 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN`
ZINC34273707 ZINC	1.000	256.5 Da LogP 4.37 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCCN`
ZINC5178646 ZINC	1.000	228.4 Da LogP 3.59 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCN`
ZINC3055005 ZINC	0.750	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007 ZINC	0.750	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010 ZINC	0.750	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555366 ZINC	0.714	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1555367 ZINC	0.714	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555369 ZINC	0.714	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720127 ZINC	0.714	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1720128 ZINC	0.714	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720130 ZINC	0.714	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC5113207 ZINC	0.667	217.3 Da LogP -0.10 TPSA 101.4	✓ Ro5	✓ Clean	`NCCCCNCCCC[C@H](N)C(=O)O`
ZINC1545440 ZINC	0.615	213.4 Da LogP 4.65 TPSA 26.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCN`
ZINC2385445 ZINC	0.615	201.4 Da LogP 2.84 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCO`
ZINC34196183 ZINC	0.615	229.4 Da LogP 3.62 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCO`
ZINC38585283 ZINC	0.615	203.4 Da LogP 3.39 TPSA 26.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCS`
ZINC2561080 ZINC	0.586	246.3 Da LogP -1.64 TPSA 144.5	✓ Ro5	✓ Clean	`NCCC[C@H](N)C(=O)N[C@@H](CCCN)C(=O)O`
ZINC15261541 ZINC	0.581	261.3 Da LogP -1.51 TPSA 155.7	✓ Ro5	✓ Clean	`NCCC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC1570993 ZINC	0.577	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@H](N)C(=O)O`
ZINC1570999 ZINC	0.577	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1620974 ZINC	0.577	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1742220 ZINC	0.577	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@H](N)C(=O)O`
ZINC2035155 ZINC	0.577	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@@H](N)C(=O)O`
ZINC2035157 ZINC	0.577	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](N)C(=O)O`
ZINC2037129 ZINC	0.577	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC2106542 ZINC	0.577	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2106543 ZINC	0.577	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2108713 ZINC	0.577	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCC(=O)O)C(=O)O`
ZINC2108714 ZINC	0.577	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCC(=O)O)C(=O)O`
ZINC43531622 ZINC	0.577	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC43531626 ZINC	0.577	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC5113209 ZINC	0.577	275.3 Da LogP -0.26 TPSA 138.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC8437446 ZINC	0.577	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC1598087 ZINC	0.571	215.4 Da LogP 1.61 TPSA 64.1	✓ Ro5	✓ Clean	`NCCCCCCNCCCCCCN`
ZINC205048564 ZINC	0.548	260.3 Da LogP -1.25 TPSA 144.5	✓ Ro5	✓ Clean	`NCCCC[C@H](N)C(=O)N[C@@H](CCCN)C(=O)O`
ZINC4899571 ZINC	0.548	360.5 Da LogP -2.42 TPSA 199.6	1 viol.	✓ Clean	`NCCC[C@H](N)C(=O)N[C@@H](CCCN)C(=O)N[C@@H](CCCN…`
ZINC20112808 ZINC	0.536	211.2 Da LogP -0.25 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@H](CCCCP(=O)(O)O)C(=O)O`
ZINC2169486 ZINC	0.536	211.2 Da LogP -0.25 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@@H](CCCCP(=O)(O)O)C(=O)O`
ZINC1856281 ZINC	0.517	225.2 Da LogP 0.14 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@H](CCCCCP(=O)(O)O)C(=O)O`
ZINC19364679 ZINC	0.517	233.3 Da LogP -1.43 TPSA 138.7	✓ Ro5	✓ Clean	`N[C@@H](CNCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC2139781 ZINC	0.517	269.2 Da LogP -0.41 TPSA 158.2	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](C(=O)O)P(=O)(O)O)C(=O)O`
ZINC2139783 ZINC	0.517	269.2 Da LogP -0.41 TPSA 158.2	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](C(=O)O)P(=O)(O)O)C(=O)O`
ZINC2139784 ZINC	0.517	269.2 Da LogP -0.41 TPSA 158.2	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](C(=O)O)P(=O)(O)O)C(=O)O`
ZINC2139785 ZINC	0.517	269.2 Da LogP -0.41 TPSA 158.2	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@H](C(=O)O)P(=O)(O)O)C(=O)O`
ZINC2149821 ZINC	0.517	239.2 Da LogP 0.53 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCP(=O)(O)O)C(=O)O`
ZINC2149823 ZINC	0.517	239.2 Da LogP 0.53 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@H](CCCCCCP(=O)(O)O)C(=O)O`
ZINC2516019 ZINC	0.517	225.2 Da LogP 0.14 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@@H](CCCCCP(=O)(O)O)C(=O)O`
ZINC95621421 ZINC	0.517	233.3 Da LogP -1.43 TPSA 138.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC[C@H](N)C(=O)O)C(=O)O`
ZINC95621422 ZINC	0.517	233.3 Da LogP -1.43 TPSA 138.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC[C@@H](N)C(=O)O)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.