Protein profile

KP13_05545

Acetylornithine deacetylase

Genome: KpKP13

Gene: AHE44551.1 argE Structure source: AlphaFold + ColabFold UniProt A0A0H3GXL0

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Amino acids 380

Annotations 5

Features 15

PDB binders 6

Druggability 0.416

Overview

Basic information about this protein and its source genome.

Accession: KP13_05545
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44551.1 argE
Status: annotated
Amino acids: 380
Structure source: AlphaFold + ColabFold

3.5.1.18

GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0046872 Binding to a metal ion. GO:0009014 Catalysis of the reaction: N-succinyl-LL-2,6-diaminopimelate + H2O = LL-2,6-diaminopimelate + succinate. GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 23.625
Human E-value: 2.21e-08
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 96.05

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 0.416

Structure A0A0H3GXL0

Pocket Pocket 5

P2Rank 0.388

Structure A0A0H3GXL0

Pocket Pocket 1

ColabFold model

FPocket 0.473 · Pocket 3

P2Rank 0.417 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 11 / 4744 genomes with a hit

Normalized 0.002

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

3.5.1.18

Gene Ontology (GO)

GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0046872 Binding to a metal ion.
GO:0009014 Catalysis of the reaction: N-succinyl-LL-2,6-diaminopimelate + H2O = LL-2,6-diaminopimelate + succinate.
GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
6	365	CDD	cd08659	M20_ArgE_DapE-like
6	356	NCBIfam	TIGR01910	ArgE/DapE family deacylase
6	356	InterPro	IPR010182	N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine deformylase/Succinyl-diaminopimelate desuccinylase
66	75	ProSitePatterns	PS00758	ArgE / dapE / ACY1 / CPG2 / yscS family signature 1.
66	75	InterPro	IPR001261	ArgE/DapE/ACY1/CPG2/YscS, conserved site
174	270	SUPERFAMILY	SSF55031	Bacterial exopeptidase dimerisation domain
174	270	InterPro	IPR036264	Bacterial exopeptidase dimerisation domain
3	368	SUPERFAMILY	SSF53187	Zn-dependent exopeptidases
174	282	Gene3D	G3DSA:3.30.70.360	-
11	354	Gene3D	G3DSA:3.40.630.10	Zn peptidases
67	366	Pfam	PF01546	Peptidase family M20/M25/M40
67	366	InterPro	IPR002933	Peptidase M20
5	368	PANTHER	PTHR43808	ACETYLORNITHINE DEACETYLASE
170	271	Pfam	PF07687	Peptidase dimerisation domain
170	271	InterPro	IPR011650	Peptidase M20, 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_A0A0H3GXL0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05545	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
5				0.416
4				0.341

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				5.79	0.282
2				2.67	0.079

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				0.473

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	6.18	0.308
2	3.2	0.11
3	0.89	0.004

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.

56 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
6R6	5K8N	D3WZ85	182.1 Da LogP 0.88 TPSA 106.5	✓ Ro5	✓ Clean	`c1cc(c(cc1[N+](=O)[O-])C(=O)O)N`
6R7	5K8O	D3WZ85	183.1 Da LogP 1.00 TPSA 100.7	✓ Ro5	✓ Clean	`c1cc(c(cc1[N+](=O)[O-])C(=O)O)O`
6R8	5K8P	D3WZ85	200.2 Da LogP -0.79 TPSA 126.7	✓ Ro5	✓ Clean	`C1C=C(C=C([C@]1(N)O)C(=O)O)[N+](=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`
ZINC157056	0.750	211.1 Da LogP 0.99 TPSA 117.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc([N+](=O)[O-])cc1C(=O)O`
ZINC56845	0.733	246.0 Da LogP 2.06 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc([N+](=O)[O-])ccc1Br`
ZINC1717037	0.724	332.2 Da LogP 2.57 TPSA 160.9	✓ Ro5	✓ Clean	`O=C(O)c1cc([N+](=O)[O-])ccc1-c1ccc([N+](=O)[O-]…`
ZINC3861498	0.719	242.2 Da LogP 2.41 TPSA 86.2	✓ Ro5	Alert	`Nc1ccc([N+](=O)[O-])cc1C(=O)c1ccccc1`
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`
ZINC503943946	0.703	318.2 Da LogP 2.44 TPSA 150.0	✓ Ro5	✓ Clean	`O=C(O)c1cc(Nc2ccc([N+](=O)[O-])cc2C(=O)O)ccc1O`
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`
ZINC156878	0.700	201.6 Da LogP 1.95 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc([N+](=O)[O-])ccc1Cl`
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`
ZINC4404106	0.700	212.1 Da LogP 1.20 TPSA 123.6	✓ Ro5	✓ Clean	`O=C(O)c1cc([N+](=O)[O-])ccc1[N+](=O)[O-]`
ZINC100134073	0.686	287.2 Da LogP 3.41 TPSA 125.4	✓ Ro5	Alert	`O=C(O)c1cc(/N=N\c2ccc([N+](=O)[O-])cc2)ccc1O`
ZINC12358629	0.686	287.2 Da LogP 3.41 TPSA 125.4	✓ Ro5	Alert	`O=C(O)c1cc(N=Nc2ccc([N+](=O)[O-])cc2)ccc1O`
ZINC3861418	0.686	287.2 Da LogP 3.41 TPSA 125.4	✓ Ro5	Alert	`O=C(O)c1cc(/N=N/c2ccc([N+](=O)[O-])cc2)ccc1O`
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`
ZINC1757911	0.677	246.0 Da LogP 2.06 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc([N+](=O)[O-])cc1Br`
ZINC2559907	0.677	293.0 Da LogP 1.90 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc([N+](=O)[O-])ccc1I`
ZINC208845	0.676	233.2 Da LogP 2.15 TPSA 100.7	✓ Ro5	✓ Clean	`O=C(O)c1cc2cc([N+](=O)[O-])ccc2cc1O`
ZINC43190938	0.676	416.3 Da LogP 1.51 TPSA 167.4	✓ Ro5	✓ Clean	`O=C(c1cc([N+](=O)[O-])ccc1O)N1CCN(C(=O)c2cc([N+…`
ZINC1556249	0.667	332.2 Da LogP 2.57 TPSA 160.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc([N+](=O)[O-])cc1-c1cc([N+](=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`
ZINC4240517	0.657	257.2 Da LogP 2.43 TPSA 98.3	✓ Ro5	✓ Clean	`Nc1ccc([N+](=O)[O-])cc1C(=O)Nc1ccccc1`
ZINC2523035	0.656	225.2 Da LogP 0.92 TPSA 117.7	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc([N+](=O)[O-])cc1C(=O)O`
ZINC1570993	0.652	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[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`
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`
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`

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.