Protein target profile

KP13_02722

Agmatinase

Genome: KpKP13 Gene: speB AHE42710.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H2T8
Length 306
Pocket druggability 0.676
Direct ligand evidence 0 162 total records
Functional annotation 0 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.

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 (%)
41.096 Lower values reduce human off-target concern.
Human E-value
1.14e-63
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
51.311 Higher values support similarity to known essential genes.
DEG E-value
3.2e-89 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
98.3 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 0.676
Structure A0A0H3H2T8
Pocket Pocket 7
P2Rank 0.466
Structure A0A0H3H2T8
Pocket Pocket 1
ColabFold model
FPocket 0.637 · Pocket 2
P2Rank 0.546 · 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.

Chemistry

ChEMBL CHEMBL4764455 ChEMBL CHEMBL4745275 ChEMBL CHEMBL1812661 ChEMBL CHEMBL5723327 ChEMBL CHEMBL4749355 ChEMBL CHEMBL5807059 ChEMBL CHEMBL4757930 ChEMBL CHEMBL4752307 ChEMBL CHEMBL4752391 ChEMBL CHEMBL4753285 ChEMBL CHEMBL2418831 ChEMBL CHEMBL4750174 ChEMBL CHEMBL4778086 ChEMBL CHEMBL2418830 ChEMBL CHEMBL4244287 ChEMBL CHEMBL2418991 ChEMBL CHEMBL2418829 ChEMBL CHEMBL2418998 ChEMBL NNH ChEMBL CHEMBL2326090 ChEMBL CHEMBL2418999 ChEMBL CHEMBL2418828 ChEMBL CHEMBL539140 ChEMBL CHEMBL4793482 ChEMBL CHEMBL5171566 ChEMBL CHEMBL5853762 ChEMBL CHEMBL2326087 ChEMBL CHEMBL5955172 ChEMBL CHEMBL5170454 ChEMBL CHEMBL5192755 ChEMBL CHEMBL6012295 ChEMBL CHEMBL2418993 ChEMBL CHEMBL2418994 ChEMBL CHEMBL6014233 ChEMBL CHEMBL2418995 ChEMBL CHEMBL5921659 ChEMBL CHEMBL2326085 ChEMBL CHEMBL5774581 ChEMBL CHEMBL2418996 ChEMBL CHEMBL5275544 ChEMBL CHEMBL4218271 ChEMBL CHEMBL5276302 ChEMBL CHEMBL5723330 ChEMBL CHEMBL2326095 ChEMBL CHEMBL5741687 ChEMBL CHEMBL5871359 ChEMBL CHEMBL2326086 ChEMBL CHEMBL2418997 ChEMBL CHEMBL4746323 ChEMBL CHEMBL2326097 ChEMBL CHEMBL5887697 ChEMBL CHEMBL2326084 ChEMBL CHEMBL2326093 ChEMBL CHEMBL4749434 ChEMBL CHEMBL4750602 ChEMBL CHEMBL4755855 ChEMBL CHEMBL2326089 ChEMBL CHEMBL4743587 ChEMBL CHEMBL2326099 ChEMBL CHEMBL5963400 ChEMBL CHEMBL2326096 ChEMBL CHEMBL2348486 ChEMBL CHEMBL4440992 ChEMBL CHEMBL4553794 ChEMBL CHEMBL4573202 ChEMBL CHEMBL5741116 ChEMBL CHEMBL5743998 ChEMBL CHEMBL5748082 ChEMBL CHEMBL5751054 ChEMBL CHEMBL5813246 ChEMBL CHEMBL5819053 ChEMBL CHEMBL5836988 ChEMBL CHEMBL5863488 ChEMBL CHEMBL5869739 ChEMBL CHEMBL5875670 ChEMBL CHEMBL5890073 ChEMBL CHEMBL5902643 ChEMBL CHEMBL5929479 ChEMBL CHEMBL5929671 ChEMBL CHEMBL5936717 ChEMBL CHEMBL5956917 ChEMBL CHEMBL6009962 ChEMBL CHEMBL6012461 ChEMBL CHEMBL6035831 ChEMBL CHEMBL6039146 ChEMBL CHEMBL6057874 ChEMBL CHEMBL6058456 ChEMBL CHEMBL2418992 ChEMBL CHEMBL5990198 ChEMBL CHEMBL5822048 ChEMBL CHEMBL2348488 ChEMBL CHEMBL2348487 ChEMBL CHEMBL5744965 ChEMBL CHEMBL5749833 ChEMBL CHEMBL5801265 ChEMBL CHEMBL5806072 ChEMBL CHEMBL5837269 ChEMBL CHEMBL5847950 ChEMBL CHEMBL5850215 ChEMBL CHEMBL5899394

Sequence

Primary amino-acid sequence viewer.

MSTLGHQYDNSLVSNAFGFLRLPMNFMPYESDADWVITGVPFDMATSGRAGGRHGPAAIRQVSTNLAWEHNRFPWNFDMRERLNVVDCGDLVYAFGDAREMSEKLQAHAEKLLAAGKRMLSFGGDHFVTLPLLRAHAKHFGKMALVHFDAHTDTYANGCEFDHGTMFYTAPNEGLIDPNHSVQIGIRTEFDKDNGFTVLDAGQVNDRSVDDVIAQVKQIVGDMPVYLTFDIDCLDPAFAPGTGTPVIGGLTSDRAIKLVRGLKDLNIVGMDVVEVAPAYDQSEITALAAATLALEMLYIQAAKKGE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0009446 The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane; putrescine can be synthesized from arginine or ornithine and is the metabolic precursor of spermidine and spermine.
  • 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:0030145 Binding to a manganese ion (Mn).
  • GO:0046872 Binding to a metal ion.
  • GO:0008783 Catalysis of the reaction: agmatine + H2O = putrescine + urea.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
22 299 NCBIfam TIGR01230 agmatinase
22 299 InterPro IPR005925 Agmatinase-related
13 301 SUPERFAMILY SSF52768 Arginase/deacetylase
13 301 InterPro IPR023696 Ureohydrolase domain superfamily
3 304 FunFam G3DSA:3.40.800.10:FF:000001 Agmatinase
1 304 Hamap MF_01418 Agmatinase [speB].
1 304 InterPro IPR023694 Agmatinase
34 296 Pfam PF00491 Arginase family
34 296 InterPro IPR006035 Ureohydrolase
19 284 CDD cd11592 Agmatinase_PAH
19 302 PANTHER PTHR11358 ARGINASE/AGMATINASE
19 302 InterPro IPR006035 Ureohydrolase
228 249 ProSitePatterns PS01053 Arginase family signature.
228 249 InterPro IPR020855 Ureohydrolase, manganese-binding site
4 305 Gene3D G3DSA:3.40.800.10 Ureohydrolase domain
21 306 ProSiteProfiles PS51409 Arginase family profile.
21 306 InterPro IPR006035 Ureohydrolase
13 304 PIRSF PIRSF036979 Arginase
13 304 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 #7
0.676
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #3
0.324
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.466
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.058
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:126-126
UniProt: Binding site:149-149
UniProt: Binding site:151-151
UniProt: Binding site:153-153
UniProt: Binding site:230-230
UniProt: Binding site:232-232
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_A0A0H3H2T8
AlphaFold DB full sequence Viewing
ColabFold KP13_02722
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.

162 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 112 records from similar proteins
Structural ligands 12 0 loaded crystals
Measured bioactivity 100 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
1EC PDB via homolog Detail RCSB PDB
1EE PDB via homolog Detail RCSB PDB
38I PDB via homolog Detail RCSB PDB
BEN PDB via homolog Detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
16D RCSB PDB Q9I6K2 116.2 Da LogP 0.46 TPSA 52.0 ✓ Ro5 ✓ Clean C(CCCN)CCN
1EC RCSB PDB P78540 250.1 Da LogP -1.37 TPSA 144.2 1 viol. ✓ Clean [B-](CCCC[C@@](CCCO)(C(=O)O)N)(O)(O)O
1EE RCSB PDB P78540 319.2 Da LogP -1.30 TPSA 147.5 1 viol. ✓ Clean [B-](CCCC[C@@](CCN1CCC(CC1)O)(C(=O)O)N)(O)(O)O
38I RCSB PDB P78540 460.2 Da LogP 2.60 TPSA 127.3 ✓ Ro5 ✓ Clean [B-](CCCC[C@@](C1C[C@H]2CC[C@@H](C1)N2Cc3ccc(c(…
BEN RCSB PDB P78540 120.2 Da LogP 0.97 TPSA 49.9 ✓ Ro5 ✓ Clean [H]/N=C(\c1ccccc1)/N
HDQ RCSB PDB P78540 330.2 Da LogP -1.46 TPSA 139.3 1 viol. ✓ Clean [B-](CCC[C@H]1CN(C[C@]1(C(=O)O)N)C[C@@H]2CCCCN2…
HE8 RCSB PDB P78540 233.1 Da LogP -2.32 TPSA 136.0 1 viol. ✓ Clean [B-](CCC[C@H]1CNC[C@]1(C(=O)O)N)(O)(O)O
ORN RCSB PDB P46637 132.2 Da LogP -0.86 TPSA 89.3 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)N)CN
S2C RCSB PDB P78540 210.0 Da LogP -1.95 TPSA 124.0 ✓ Ro5 ✓ Clean [B-](CCSC[C@@H](C(=O)O)N)(O)(O)O
X7A RCSB PDB P78540 303.2 Da LogP -0.27 TPSA 127.3 ✓ Ro5 ✓ Clean [B-](CCCC[C@@](CCN1CCCCC1)(C(=O)O)N)(O)(O)O
X8A RCSB PDB P78540 317.2 Da LogP -0.01 TPSA 113.3 ✓ Ro5 ✓ Clean [B-](CCCC[C@@](CCN1CCCCC1)(C(=O)O)NC)(O)(O)O
XA1 RCSB PDB P78540 399.7 Da LogP 1.42 TPSA 127.3 ✓ Ro5 ✓ Clean [B-](CCCC[C@@](C1CCN(CC1)Cc2ccc(cc2)Cl)(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.