Protein profile

KP13_15895

Agmatinase

Genome: KpKP13

Gene: ANJ86590.1 Structure source: AlphaFold + ColabFold UniProt A0A6A8ECW2

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Amino acids 316

Annotations 6

Features 21

PDB binders 3

Druggability 0.531

Overview

Basic information about this protein and its source genome.

Accession: KP13_15895
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ANJ86590.1
Status: annotated
Amino acids: 316
Structure source: AlphaFold + ColabFold

3.5.3.11

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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 61.364
Human E-value: 5.34e-136
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 43.098
DEG E-value: 1.5199999999999999e-61
Localization: Cytoplasmic
ColabFold pLDDT: 97.3

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its 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

Normalized 0.005

Sequence

Primary amino-acid sequence viewer.

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A6A8ECW2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_15895	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
3				0.531

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				8.54	0.456

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.264
11				0.225

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				8.21	0.437

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

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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	3NIP	Q9I6K2	116.2 Da LogP 0.46 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCCN)CCN`
CAC	3M1R	P42068	137.0 Da LogP -0.52 TPSA 40.1	✓ Ro5	✓ Clean	`C[As](=O)(C)[O-]`
ORN	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	1.000	200.4 Da LogP 2.80 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN`
ZINC34273707	1.000	256.5 Da LogP 4.37 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCCN`
ZINC5178646	1.000	228.4 Da LogP 3.59 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCN`
ZINC3055005	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	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	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	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	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	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	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	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	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	0.667	217.3 Da LogP -0.10 TPSA 101.4	✓ Ro5	✓ Clean	`NCCCCNCCCC[C@H](N)C(=O)O`
ZINC1545440	0.615	213.4 Da LogP 4.65 TPSA 26.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCN`
ZINC2385445	0.615	201.4 Da LogP 2.84 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCO`
ZINC34196183	0.615	229.4 Da LogP 3.62 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCO`
ZINC38585283	0.615	203.4 Da LogP 3.39 TPSA 26.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCS`
ZINC2561080	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	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	0.577	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@H](N)C(=O)O`
ZINC1570999	0.577	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1620974	0.577	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1742220	0.577	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@H](N)C(=O)O`
ZINC2035155	0.577	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@@H](N)C(=O)O`
ZINC2035157	0.577	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](N)C(=O)O`
ZINC2037129	0.577	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC2106542	0.577	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2106543	0.577	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2108713	0.577	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCC(=O)O)C(=O)O`
ZINC2108714	0.577	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCC(=O)O)C(=O)O`
ZINC43531622	0.577	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC43531626	0.577	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC5113209	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	0.577	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC1598087	0.571	215.4 Da LogP 1.61 TPSA 64.1	✓ Ro5	✓ Clean	`NCCCCCCNCCCCCCN`
ZINC205048564	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	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	0.536	211.2 Da LogP -0.25 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@H](CCCCP(=O)(O)O)C(=O)O`
ZINC2169486	0.536	211.2 Da LogP -0.25 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@@H](CCCCP(=O)(O)O)C(=O)O`
ZINC1856281	0.517	225.2 Da LogP 0.14 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@H](CCCCCP(=O)(O)O)C(=O)O`
ZINC19364679	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	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	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	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	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	0.517	239.2 Da LogP 0.53 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCP(=O)(O)O)C(=O)O`
ZINC2149823	0.517	239.2 Da LogP 0.53 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@H](CCCCCCP(=O)(O)O)C(=O)O`
ZINC2516019	0.517	225.2 Da LogP 0.14 TPSA 120.9	✓ Ro5	✓ Clean	`N[C@@H](CCCCCP(=O)(O)O)C(=O)O`
ZINC95621421	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	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.