Protein profile

VK055_3230

acetylornithine deacetylase

Genome: KpATCC43816

Gene: argE AIK81791.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLH2

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Amino acids 383

Annotations 7

Features 20

PDB binders 4

Druggability 0.583

Overview

Basic information about this protein and its source genome.

Accession: VK055_3230
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: argE AIK81791.1
Status: annotated
Amino acids: 383
Structure source: AlphaFold + ColabFold

3.5.1.16

GO:0019213 Catalysis of the hydrolysis of an acetyl group from a substrate molecule. GO:0006526 The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0008777 Catalysis of the reaction: N2-acetyl-L-ornithine + H2O = acetate + L-ornithine. GO:0008270 Binding to a zinc ion (Zn).

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 31.25
Localization: Cytoplasmic
ColabFold pLDDT: 96.54

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 0.583

Structure A0A0H3GLH2

Pocket Pocket 1

P2Rank 0.682

Structure A0A0H3GLH2

Pocket Pocket 1

ColabFold model

FPocket 0.374 · Pocket 14

P2Rank 0.53 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 131 / 4744 genomes with a hit

Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

3.5.1.16

Gene Ontology (GO)

GO:0019213 Catalysis of the hydrolysis of an acetyl group from a substrate molecule.
GO:0006526 The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0008777 Catalysis of the reaction: N2-acetyl-L-ornithine + H2O = acetate + L-ornithine.
GO:0008270 Binding to a zinc ion (Zn).

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
75	84	ProSitePatterns	PS00758	ArgE / dapE / ACY1 / CPG2 / yscS family signature 1.
75	84	InterPro	IPR001261	ArgE/DapE/ACY1/CPG2/YscS, conserved site
10	377	NCBIfam	TIGR01892	acetylornithine deacetylase
10	377	InterPro	IPR010169	Acetylornithine deacetylase ArgE
3	381	SUPERFAMILY	SSF53187	Zn-dependent exopeptidases
181	296	Gene3D	G3DSA:3.30.70.360	-
10	378	CDD	cd03894	M20_ArgE
3	381	PANTHER	PTHR43808	ACETYLORNITHINE DEACETYLASE
3	382	Hamap	MF_01108	Acetylornithine deacetylase [argE].
3	382	InterPro	IPR010169	Acetylornithine deacetylase ArgE
181	296	FunFam	G3DSA:3.30.70.360:FF:000003	Acetylornithine deacetylase
76	377	Pfam	PF01546	Peptidase family M20/M25/M40
76	377	InterPro	IPR002933	Peptidase M20
110	147	ProSitePatterns	PS00759	ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.
110	147	InterPro	IPR001261	ArgE/DapE/ACY1/CPG2/YscS, conserved site
15	363	Gene3D	G3DSA:3.40.630.10	Zn peptidases
178	287	Pfam	PF07687	Peptidase dimerisation domain
178	287	InterPro	IPR011650	Peptidase M20, dimerisation domain
181	294	SUPERFAMILY	SSF55031	Bacterial exopeptidase dimerisation domain
181	294	InterPro	IPR036264	Bacterial exopeptidase dimerisation domain

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_A0A0H3GLH2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3230	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
1				0.583
2				0.075
3				0.035
10				0.0

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	Score	Probability
1	15.8	0.682
2	1.53	0.018
3	0.97	0.005
4	0.62	0.001
5	0.57	0.0

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
8				0.011
4				0.001
6				0.001
23				0.001

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				11.5	0.53
2				1.18	0.009

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.

54 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
AEP	1LFW	P45494	239.2 Da LogP -0.26 TPSA 137.9	✓ Ro5	✓ Clean	`C[C@H](C[P@](=O)([C@H](CC(=O)O)N)O)C(=O)O`
API	5VO3	P44514	190.2 Da LogP -1.02 TPSA 126.6	✓ Ro5	✓ Clean	`C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N`
SIN	5VO3	P44514	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)O`
X8Z	4PQA	Q9JYL2	217.3 Da LogP 0.63 TPSA 57.6	✓ Ro5	✓ Clean	`C[C@H](CS)C(=O)N1CCC[C@H]1C(=O)O`

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
ZINC20226	1.000	217.3 Da LogP 0.63 TPSA 57.6	✓ Ro5	✓ Clean	`C[C@H](CS)C(=O)N1CCC[C@@H]1C(=O)O`
ZINC57000	1.000	217.3 Da LogP 0.63 TPSA 57.6	✓ Ro5	✓ Clean	`C[C@@H](CS)C(=O)N1CCC[C@H]1C(=O)O`
ZINC57001	1.000	217.3 Da LogP 0.63 TPSA 57.6	✓ Ro5	✓ Clean	`C[C@H](CS)C(=O)N1CCC[C@H]1C(=O)O`
ZINC57002	1.000	217.3 Da LogP 0.63 TPSA 57.6	✓ Ro5	✓ Clean	`C[C@@H](CS)C(=O)N1CCC[C@@H]1C(=O)O`
ZINC3055005	0.882	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	0.882	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	0.882	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	0.833	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	0.833	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	0.833	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	0.833	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	0.833	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	0.833	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC38212936	0.711	231.3 Da LogP 0.72 TPSA 46.6	✓ Ro5	✓ Clean	`COC(=O)[C@@H]1CCCN1C(=O)[C@H](C)CS`
ZINC111451008	0.703	231.3 Da LogP 1.06 TPSA 57.6	✓ Ro5	✓ Clean	`CSC[C@H](C)C(=O)N1CCC[C@H]1C(=O)O`
ZINC6036727	0.703	231.3 Da LogP 1.06 TPSA 57.6	✓ Ro5	✓ Clean	`CSC[C@@H](C)C(=O)N1CCC[C@H]1C(=O)O`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC237154739	0.684	215.2 Da LogP 0.34 TPSA 66.8	✓ Ro5	✓ Clean	`COC[C@@H](C)C(=O)N1CCC[C@H]1C(=O)O`
ZINC237231340	0.684	215.2 Da LogP 0.34 TPSA 66.8	✓ Ro5	✓ Clean	`COC[C@H](C)C(=O)N1CCC[C@H]1C(=O)O`
ZINC67664984	0.667	247.3 Da LogP 0.08 TPSA 74.7	✓ Ro5	✓ Clean	`C[C@H](C[S@](C)=O)C(=O)N1CCC[C@H]1C(=O)O`
ZINC67664986	0.667	247.3 Da LogP 0.08 TPSA 74.7	✓ Ro5	✓ Clean	`C[C@H](C[S@@](C)=O)C(=O)N1CCC[C@H]1C(=O)O`
ZINC1570993	0.652	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@H](N)C(=O)O`
ZINC1570999	0.652	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1620974	0.652	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1742220	0.652	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@H](N)C(=O)O`
ZINC2035155	0.652	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@@H](N)C(=O)O`
ZINC2035157	0.652	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](N)C(=O)O`
ZINC2037129	0.652	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC2106542	0.652	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2106543	0.652	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2108713	0.652	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCC(=O)O)C(=O)O`
ZINC2108714	0.652	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCC(=O)O)C(=O)O`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC43531622	0.652	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC43531626	0.652	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC5113209	0.652	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	0.652	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC58131	0.650	259.3 Da LogP 0.98 TPSA 74.7	✓ Ro5	✓ Clean	`CC(=O)SC[C@H](C)C(=O)N1CCC[C@H]1C(=O)O`
ZINC58132	0.650	259.3 Da LogP 0.98 TPSA 74.7	✓ Ro5	✓ Clean	`CC(=O)SC[C@@H](C)C(=O)N1CCC[C@H]1C(=O)O`
ZINC58133	0.650	259.3 Da LogP 0.98 TPSA 74.7	✓ Ro5	✓ Clean	`CC(=O)SC[C@H](C)C(=O)N1CCC[C@@H]1C(=O)O`
ZINC58134	0.650	259.3 Da LogP 0.98 TPSA 74.7	✓ Ro5	✓ Clean	`CC(=O)SC[C@@H](C)C(=O)N1CCC[C@@H]1C(=O)O`
ZINC139041101	0.643	272.4 Da LogP 0.31 TPSA 60.9	✓ Ro5	✓ Clean	`C[C@H](CS)C(=O)N1C[C@@H]2CCCN2C[C@@H]1C(=O)O`
ZINC139041329	0.643	272.4 Da LogP 0.31 TPSA 60.9	✓ Ro5	✓ Clean	`C[C@H](CS)C(=O)N1C[C@H]2CCCN2C[C@@H]1C(=O)O`
ZINC256066812	0.643	272.4 Da LogP 0.31 TPSA 60.9	✓ Ro5	✓ Clean	`C[C@H](CS)C(=O)N1C[C@H]2CCCN2C[C@H]1C(=O)O`
ZINC256066813	0.643	272.4 Da LogP 0.31 TPSA 60.9	✓ Ro5	✓ Clean	`C[C@H](CS)C(=O)N1C[C@@H]2CCCN2C[C@H]1C(=O)O`
ZINC3792809	0.634	246.3 Da LogP 1.11 TPSA 87.0	✓ Ro5	✓ Clean	`C[C@H](CSN=O)C(=O)N1CCC[C@H]1C(=O)O`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=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.