Protein profile

KP13_03831

Succinyl-diaminopimelate desuccinylase

Genome: KpKP13

Gene: dapE AHE43315.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H1C2

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Amino acids 375

Annotations 9

Features 22

PDB binders 4

Druggability 0.44

Overview

Basic information about this protein and its source genome.

Accession: KP13_03831
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: dapE AHE43315.1
Status: annotated
Amino acids: 375
Structure source: AlphaFold + ColabFold

3.5.1.18

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. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0008777 Catalysis of the reaction: N2-acetyl-L-ornithine + H2O = acetate + L-ornithine. GO:0050897 Binding to a cobalt ion (Co2+). GO:0008270 Binding to a zinc ion (Zn).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 42.857
Human E-value: 2.76e-07
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 92.0
DEG E-value: 0.0
Localization: Unknown
ColabFold pLDDT: 97.08

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 0.44

Structure A0A0H3H1C2

Pocket Pocket 3

P2Rank 0.476

Structure A0A0H3H1C2

Pocket Pocket 1

ColabFold model

FPocket 0.442 · Pocket 1

P2Rank 0.458 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 200 / 4744 genomes with a hit

Normalized 0.042

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

3.5.1.18

Gene Ontology (GO)

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.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0008777 Catalysis of the reaction: N2-acetyl-L-ornithine + H2O = acetate + L-ornithine.
GO:0050897 Binding to a cobalt ion (Co2+).
GO:0008270 Binding to a zinc ion (Zn).
GO:0019877 OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
GO:0006526 The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
256	375	Gene3D	G3DSA:3.40.630.10	Zn peptidases
61	70	ProSitePatterns	PS00758	ArgE / dapE / ACY1 / CPG2 / yscS family signature 1.
61	70	InterPro	IPR001261	ArgE/DapE/ACY1/CPG2/YscS, conserved site
179	289	FunFam	G3DSA:3.30.70.360:FF:000011	Succinyl-diaminopimelate desuccinylase
255	375	FunFam	G3DSA:3.40.630.10:FF:000010	Succinyl-diaminopimelate desuccinylase
3	244	Gene3D	G3DSA:3.40.630.10	Zn peptidases
6	373	NCBIfam	TIGR01246	succinyl-diaminopimelate desuccinylase
6	373	InterPro	IPR005941	Succinyl-diaminopimelate desuccinylase, proteobacteria
3	244	FunFam	G3DSA:3.40.630.10:FF:000005	Succinyl-diaminopimelate desuccinylase
5	373	PANTHER	PTHR43808	ACETYLORNITHINE DEACETYLASE
97	136	ProSitePatterns	PS00759	ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.
97	136	InterPro	IPR001261	ArgE/DapE/ACY1/CPG2/YscS, conserved site
62	371	Pfam	PF01546	Peptidase family M20/M25/M40
62	371	InterPro	IPR002933	Peptidase M20
175	280	Pfam	PF07687	Peptidase dimerisation domain
175	280	InterPro	IPR011650	Peptidase M20, dimerisation domain
6	370	CDD	cd03891	M20_DapE_proteobac
3	375	Hamap	MF_01690	Succinyl-diaminopimelate desuccinylase [dapE].
3	375	InterPro	IPR005941	Succinyl-diaminopimelate desuccinylase, proteobacteria
179	287	SUPERFAMILY	SSF55031	Bacterial exopeptidase dimerisation domain
179	287	InterPro	IPR036264	Bacterial exopeptidase dimerisation domain
5	373	SUPERFAMILY	SSF53187	Zn-dependent exopeptidases

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_A0A0H3H1C2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03831	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				0.44

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				4.94	0.223

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				0.442

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				4.19	0.17

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
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`
BES	4RUH	Q96KP4	308.4 Da LogP 0.53 TPSA 112.7	✓ Ro5	✓ Clean	`CC(C)C[C@@H](C(=O)O)NC(=O)[C@H]([C@@H](Cc1ccccc…`
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
ZINC11592554	1.000	308.4 Da LogP 0.53 TPSA 112.6	✓ Ro5	✓ Clean	`CC(C)C[C@@H](NC(=O)[C@@H](O)[C@@H](N)Cc1ccccc1)…`
ZINC11592555	1.000	308.4 Da LogP 0.53 TPSA 112.6	✓ Ro5	✓ Clean	`CC(C)C[C@@H](NC(=O)[C@H](O)[C@@H](N)Cc1ccccc1)C…`
ZINC11592556	1.000	308.4 Da LogP 0.53 TPSA 112.6	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@H](O)[C@@H](N)Cc1ccccc1)C(…`
ZINC1532730	1.000	308.4 Da LogP 0.53 TPSA 112.6	✓ Ro5	✓ Clean	`CC(C)C[C@@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccccc1)C…`
ZINC1542895	1.000	308.4 Da LogP 0.53 TPSA 112.6	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccccc1)C(…`
ZINC1558987	1.000	308.4 Da LogP 0.53 TPSA 112.6	✓ Ro5	✓ Clean	`CC(C)C[C@@H](NC(=O)[C@H](O)[C@H](N)Cc1ccccc1)C(…`
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`
ZINC2545165	1.000	308.4 Da LogP 0.53 TPSA 112.6	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@H](O)[C@H](N)Cc1ccccc1)C(=…`
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`
ZINC7996813	1.000	308.4 Da LogP 0.53 TPSA 112.6	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@@H](O)[C@@H](N)Cc1ccccc1)C…`
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`
ZINC95572961	0.829	321.4 Da LogP 0.19 TPSA 104.5	✓ Ro5	✓ Clean	`CNC(=O)[C@H](CC(C)C)NC(=O)[C@@H](O)[C@H](N)Cc1c…`
ZINC1573805	0.810	324.4 Da LogP 0.24 TPSA 132.9	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccc(O)cc1…`
ZINC17125728	0.810	324.4 Da LogP 0.24 TPSA 132.9	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@@H](O)[C@@H](N)Cc1ccc(O)cc…`
ZINC17125733	0.810	324.4 Da LogP 0.24 TPSA 132.9	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@H](O)[C@@H](N)Cc1ccc(O)cc1…`
ZINC5759636	0.810	324.4 Da LogP 0.24 TPSA 132.9	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@H](O)[C@H](N)Cc1ccc(O)cc1)…`
ZINC2390944	0.756	278.4 Da LogP 1.17 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@@H](N)Cc1ccccc1)C(=O)O`
ZINC6049599	0.756	278.4 Da LogP 1.17 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](NC(=O)[C@@H](N)Cc1ccccc1)C(=O)O`
ZINC2391109	0.750	307.3 Da LogP 1.55 TPSA 103.7	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@@H](Cc1ccccc1)C(=O)O)C(=O)O`
ZINC27727766	0.750	307.3 Da LogP 1.55 TPSA 103.7	✓ Ro5	✓ Clean	`CC(C)C[C@@H](NC(=O)[C@@H](Cc1ccccc1)C(=O)O)C(=O…`
ZINC27727773	0.750	307.3 Da LogP 1.55 TPSA 103.7	✓ Ro5	✓ Clean	`CC(C)C[C@@H](NC(=O)[C@H](Cc1ccccc1)C(=O)O)C(=O)O`
ZINC4899476	0.750	307.3 Da LogP 1.55 TPSA 103.7	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)C(=O)O)C(=O)O`
ZINC27644022	0.721	294.4 Da LogP 0.29 TPSA 112.6	✓ Ro5	✓ Clean	`CCC[C@H](NC(=O)[C@H](O)[C@H](N)Cc1ccccc1)C(=O)O`
ZINC6003711	0.711	441.5 Da LogP 0.87 TPSA 141.7	✓ Ro5	✓ Clean	`CC(C)[C@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccccc1)C(=…`
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`
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`
ZINC4899773	0.682	391.5 Da LogP 1.70 TPSA 121.5	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](…`
ZINC1569745	0.674	278.4 Da LogP 1.17 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](Cc1ccccc1)C(=O)O`
ZINC1569746	0.674	278.4 Da LogP 1.17 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@@H](Cc1ccccc1)C(=O)O`
ZINC1569747	0.674	278.4 Da LogP 1.17 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](Cc1ccccc1)C(=O)O`
ZINC1569748	0.674	278.4 Da LogP 1.17 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@H](Cc1ccccc1)C(=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`
ZINC2983230	0.659	320.4 Da LogP 1.35 TPSA 95.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](Cc1ccccc1)C(=O)N[C@@H](CC(C)C)C(=O…`
ZINC2983231	0.659	320.4 Da LogP 1.35 TPSA 95.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](Cc1ccccc1)C(=O)N[C@H](CC(C)C)C(=O)O`
ZINC2983232	0.659	320.4 Da LogP 1.35 TPSA 95.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](CC(C)C)C(=…`
ZINC2983233	0.659	320.4 Da LogP 1.35 TPSA 95.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@H](CC(C)C)C(=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.