Protein profile

PA1254

dihydrodipicolinate synthetase

Genome: NC_002516.2

Gene: PA1254 Structure source: AlphaFold UniProt Q9I490

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Amino acids 305

Annotations 4

Features 19

PDB binders 8

Druggability 0.259

Overview

Basic information about this protein and its source genome.

Accession: PA1254
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA1254
Status: annotated
Amino acids: 305
Structure source: AlphaFold

GO:0047425 Catalysis of the reaction: 4-hydroxy-1-pyrroline-2-carboxylate + H2O + H+ = 2,5-dioxopentanoate + NH4. GO:0008840 Catalysis of the reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H+. GO:0019470 The chemical reactions and pathways resulting in the breakdown of trans-4-hydroxy-L-proline. GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 27.984
Human E-value: 4.03e-19
Gut microbiome off-target: hit
Essential (DEG): N
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 0.259

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:0047425 Catalysis of the reaction: 4-hydroxy-1-pyrroline-2-carboxylate + H2O + H+ = 2,5-dioxopentanoate + NH4.
GO:0008840 Catalysis of the reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H+.
GO:0019470 The chemical reactions and pathways resulting in the breakdown of trans-4-hydroxy-L-proline.
GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
4	295	Gene3D	G3DSA:3.20.20.70	Aldolase class I
4	295	InterPro	IPR013785	Aldolase-type TIM barrel
4	295	FunFam	G3DSA:3.20.20.70:FF:000281	Probable dihydrodipicolinate synthetase
8	291	Pfam	PF00701	Dihydrodipicolinate synthetase family
8	291	InterPro	IPR002220	DapA-like
3	301	PIRSF	PIRSF001365	DHDPS
3	301	InterPro	IPR002220	DapA-like
10	290	CDD	cd00408	DHDPS-like
6	294	SMART	SM01130	DHDPS_2
6	294	InterPro	IPR002220	DapA-like
3	292	SUPERFAMILY	SSF51569	Aldolase
4	293	PANTHER	PTHR12128	DIHYDRODIPICOLINATE SYNTHASE
4	293	InterPro	IPR002220	DapA-like
40	61	PRINTS	PR00146	Dihydrodipicolinate synthase signature
40	61	InterPro	IPR002220	DapA-like
76	94	PRINTS	PR00146	Dihydrodipicolinate synthase signature
76	94	InterPro	IPR002220	DapA-like
133	150	PRINTS	PR00146	Dihydrodipicolinate synthase signature
133	150	InterPro	IPR002220	DapA-like

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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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 PA1254	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
1				0.259
3				0.215

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.

59 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
GXP	4OE7	P75682	146.1 Da LogP -1.41 TPSA 91.7	✓ Ro5	✓ Clean	`C([C@@H](C=O)O)C(=O)C(=O)O`
GXT	4OE7	P75682	58.0 Da LogP -0.62 TPSA 34.1	✓ Ro5	✓ Clean	`C(=O)C=O`
GXV	4PTN	P75682	90.1 Da LogP -1.46 TPSA 57.5	✓ Ro5	✓ Clean	`C([C@@H](C=O)O)O`
KDG	4ONV	P75682	178.1 Da LogP -2.26 TPSA 115.1	✓ Ro5	✓ Clean	`C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O`
MLT	3IRD	A5I6N2	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)C(=O)O`
PYR	3I7S	P0A6L2	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)C(=O)O`
RSH	3NEV	P75682	180.2 Da LogP -2.46 TPSA 118.2	✓ Ro5	✓ Clean	`C([C@H]([C@@H](CO)O)O)[C@@H](C(=O)O)O`
TLA	5T26	P0A6L2	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@@H]([C@H](C(=O)O)O)(C(=O)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL456197	P0A6L2	—	226.2 Da LogP 0.79 TPSA 69.7	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/C(=O)/C=C/C(=O)OCC`

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
ZINC2562361	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC3870003	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC8551322	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC8551323	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC8551324	0.739	238.2 Da LogP -3.53 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC2562359	0.708	268.2 Da LogP -4.17 TPSA 175.7	1 viol.	✓ Clean	`O=C(O)C(=O)C[C@H](O)[C@@H](O)[C@@H](O)[C@H](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`
ZINC71773891	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC32298862	0.652	226.0 Da LogP 1.50 TPSA 26.3	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/I`
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`
ZINC4975987	0.652	226.0 Da LogP 1.50 TPSA 26.3	✓ Ro5	✓ Clean	`CCOC(=O)/C=C\I`
ZINC4195949	0.630	338.4 Da LogP -0.10 TPSA 93.2	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/C(=O)N1CCN(C(=O)/C=C/C(=O)OCC)CC1`
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…`
ZINC14686444	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(=…`
ZINC115979184	0.615	200.2 Da LogP 1.45 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/C(=O)OC(C)(C)C`
ZINC136715593	0.593	304.4 Da LogP 3.67 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/C(C)=C/C=C/C=C(C)/C=C/C(=O)OCC`
ZINC2159520	0.593	274.4 Da LogP 3.53 TPSA 43.4	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/C(=O)c1c(C)c(C)c(C)c(C)c1C`
ZINC33380881	0.593	274.4 Da LogP 3.53 TPSA 43.4	✓ Ro5	✓ Clean	`CCOC(=O)/C=C\C(=O)c1c(C)c(C)c(C)c(C)c1C`
ZINC1560405156	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(\O)[C@H](O)[C@H](O)C(=O)O`
ZINC1560405157	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(/O)[C@H](O)[C@H](O)C(=O)O`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC1670412	0.577	254.3 Da LogP 2.79 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/CCCC/C=C/C(=O)OCC`
ZINC17300545	0.577	254.3 Da LogP 2.79 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C=C\CCCC/C=C/C(=O)OCC`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC8615431	0.577	254.3 Da LogP 2.79 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C=C\CCCC/C=C\C(=O)OCC`
ZINC146315135	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC1684804	0.556	217.5 Da LogP 2.48 TPSA 26.3	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/C(Cl)(Cl)Cl`
ZINC1850353	0.556	206.1 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC(O)(CC(=O)O)CC(=O)O`
ZINC2028757	0.552	215.2 Da LogP 0.50 TPSA 85.2	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/C(=N/O)C(=O)OCC`
ZINC26896999	0.552	234.2 Da LogP 1.82 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/C(F)=C(\F)C(=O)OCC`
ZINC100135524	0.542	200.2 Da LogP 1.45 TPSA 52.6	✓ Ro5	✓ Clean	`CCCOC(=O)/C=C\C(=O)OCCC`
ZINC4404469	0.542	200.2 Da LogP 1.45 TPSA 52.6	✓ Ro5	✓ Clean	`CCCOC(=O)/C=C/C(=O)OCCC`
ZINC16032383	0.536	202.2 Da LogP 1.50 TPSA 44.8	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/C(OCC)OCC`
ZINC2040347175	0.536	274.3 Da LogP 2.84 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)C=Cc1ccc(C=CC(=O)OCC)cc1`
ZINC2566170	0.536	274.3 Da LogP 2.84 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/c1ccc(/C=C/C(=O)OCC)cc1`
ZINC31318765	0.536	274.3 Da LogP 2.84 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C=C\c1ccc(/C=C\C(=O)OCC)cc1`
ZINC31318768	0.536	274.3 Da LogP 2.84 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C=C\c1ccc(/C=C/C(=O)OCC)cc1`
ZINC31628809	0.536	202.2 Da LogP 1.50 TPSA 44.8	✓ Ro5	✓ Clean	`CCOC(=O)/C=C\C(OCC)OCC`
ZINC34406087	0.536	207.1 Da LogP 1.89 TPSA 26.3	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/CCBr`
ZINC4673321	0.533	368.4 Da LogP 1.02 TPSA 110.8	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/C(=O)NCCCCCCNC(=O)/C=C/C(=O)OCC`
ZINC13398014	0.522	220.2 Da LogP -1.07 TPSA 110.1	✓ Ro5	✓ Clean	`COC(=O)CC(O)(CC(=O)OC)C(=O)O`
ZINC3861629	0.522	206.1 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C(O)(CC(=O)O)CC(=O)O`
ZINC17023506	0.517	236.2 Da LogP 2.33 TPSA 61.8	✓ Ro5	✓ Clean	`CCOC(=O)/C=C\P(=O)(OCC)OCC`
ZINC1736336	0.517	236.2 Da LogP 2.33 TPSA 61.8	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/P(=O)(OCC)OCC`
ZINC2039908434	0.516	204.2 Da LogP 1.99 TPSA 43.4	✓ Ro5	✓ Clean	`CCOC(=O)C=CC(=O)c1ccccc1`
ZINC2167059	0.516	204.2 Da LogP 1.99 TPSA 43.4	✓ Ro5	✓ Clean	`CCOC(=O)/C=C/C(=O)c1ccccc1`

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.