Protein profile

PA1162

succinyl-diaminopimelate desuccinylase

Genome: NC_002516.2

Gene: PA1162 dapE Structure source: AlphaFold UniProt Q9I4H5

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Amino acids 383

Annotations 8

Features 20

PDB binders 3

Druggability 0.676

Overview

Basic information about this protein and its source genome.

Accession: PA1162
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA1162 dapE
Status: annotated
Amino acids: 383
Structure source: AlphaFold

3.5.1.18

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0050897 Binding to a cobalt ion (Co2+). GO:0009014 Catalysis of the reaction: N-succinyl-LL-2,6-diaminopimelate + H2O = LL-2,6-diaminopimelate + succinate. 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: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 (%): 36.145
Human E-value: 3.47e-08
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 0.676

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MTASSPSLSPTLELACELIRRPSVTPLDADCQALMMRRLEAAGFALEPMRIEEVDNFWARRGGDGPVLCFAGHTDVVPTGPLQAWQHQPFDALIDDQGMLCGRGAADMKGSLASMIVAVERFVADHPEHKGAIAFLITSDEEGPAHHGTKAVVERLAARGERLDWCIVGEPSSTSLVGDVVKNGRRGSLGAKLTIRGVQGHVAYPHLAKNPIHLAAPALAELAAEHWDDGNAFFPPTSFQVSNLNSGTGATNVIPGELTALFNFRFSTESTVEGLQKRVEAILDKHGLDWHVEWALSGLPFLTEPGELLDAVAASIRAVTGRETQPSTSGGTSDGRFIATMGTQVVELGPVNATIHQVNERVLASDLELLTEIYYQTLVRLLA

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

3.5.1.18

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0050897 Binding to a cobalt ion (Co2+).
GO:0009014 Catalysis of the reaction: N-succinyl-LL-2,6-diaminopimelate + H2O = LL-2,6-diaminopimelate + succinate.
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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
9	253	Gene3D	G3DSA:3.40.630.10	Zn peptidases
265	383	Gene3D	G3DSA:3.40.630.10	Zn peptidases
12	378	CDD	cd03891	M20_DapE_proteobac
105	143	ProSitePatterns	PS00759	ArgE / dapE / ACY1 / CPG2 / yscS family signature 2.
105	143	InterPro	IPR001261	ArgE/DapE/ACY1/CPG2/YscS, conserved site
9	382	SUPERFAMILY	SSF53187	Zn-dependent exopeptidases
9	383	Hamap	MF_01690	Succinyl-diaminopimelate desuccinylase [dapE].
9	383	InterPro	IPR005941	Succinyl-diaminopimelate desuccinylase, proteobacteria
187	296	SUPERFAMILY	SSF55031	Bacterial exopeptidase dimerisation domain
187	296	InterPro	IPR036264	Bacterial exopeptidase dimerisation domain
187	297	FunFam	G3DSA:3.30.70.360:FF:000011	Succinyl-diaminopimelate desuccinylase
12	381	NCBIfam	TIGR01246	succinyl-diaminopimelate desuccinylase
12	381	InterPro	IPR005941	Succinyl-diaminopimelate desuccinylase, proteobacteria
9	252	FunFam	G3DSA:3.40.630.10:FF:000005	Succinyl-diaminopimelate desuccinylase
183	289	Pfam	PF07687	Peptidase dimerisation domain
183	289	InterPro	IPR011650	Peptidase M20, dimerisation domain
263	383	FunFam	G3DSA:3.40.630.10:FF:000010	Succinyl-diaminopimelate desuccinylase
69	379	Pfam	PF01546	Peptidase family M20/M25/M40
69	379	InterPro	IPR002933	Peptidase M20
9	381	PANTHER	PTHR43808	ACETYLORNITHINE DEACETYLASE

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 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA1162	AlphaFold	—	—	full sequence	—	Viewing

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
4				0.676
2				0.39

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
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`
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`
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`
ZINC136486150	0.625	229.3 Da LogP 0.73 TPSA 66.8	✓ Ro5	✓ Clean	`COC[C@H](C)C(=O)N1CCCC[C@@H]1C(=O)O`
ZINC136486179	0.625	229.3 Da LogP 0.73 TPSA 66.8	✓ Ro5	✓ Clean	`COC[C@@H](C)C(=O)N1CCCC[C@@H]1C(=O)O`
ZINC136486225	0.625	229.3 Da LogP 0.73 TPSA 66.8	✓ Ro5	✓ Clean	`COC[C@H](C)C(=O)N1CCCC[C@H]1C(=O)O`
ZINC136486255	0.625	229.3 Da LogP 0.73 TPSA 66.8	✓ Ro5	✓ Clean	`COC[C@@H](C)C(=O)N1CCCC[C@H]1C(=O)O`
ZINC1529497	0.615	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1700020	0.615	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=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.