Protein profile

PA2887

citronellol catabolism dehydrogenase

Genome: NC_002516.2

Gene: atuB PA2887 Structure source: Experimental + AlphaFold UniProt Q9HZW0

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Amino acids 292

Annotations 3

Features 20

PDB binders 5

Druggability 0.443

Overview

Basic information about this protein and its source genome.

Accession: PA2887
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: atuB PA2887
Status: annotated
Amino acids: 292
Structure source: Experimental + AlphaFold

1.3.1.38

GO:0019166 Catalysis of the reaction: acyl-CoA + NADP+ = trans-2,3-dehydroacyl-CoA + NADPH + H+. GO:0006633 The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 50.0
Human E-value: 1.69e-06
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 0.443

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Enzyme Commission (EC)

1.3.1.38

Gene Ontology (GO)

GO:0019166 Catalysis of the reaction: acyl-CoA + NADP+ = trans-2,3-dehydroacyl-CoA + NADPH + H+.
GO:0006633 The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
162	181	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
162	181	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
137	153	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
137	153	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
16	33	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
16	33	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
90	101	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
90	101	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
183	200	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
183	200	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
219	239	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
219	239	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
15	197	SMART	SM00822	This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group.
24	253	Pfam	PF13561	Enoyl-(Acyl carrier protein) reductase
2	264	Gene3D	G3DSA:3.40.50.720	-
12	256	CDD	cd05369	TER_DECR_SDR_a
5	260	FunFam	G3DSA:3.40.50.720:FF:000084	Short-chain dehydrogenase reductase
2	263	PANTHER	PTHR24317	PEROXISOMAL TRANS-2-ENOYL-COA REDUCTASE
13	254	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
13	254	InterPro	IPR036291	NAD(P)-binding domain superfamily

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

1 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 6LLN	X-ray	1.80 Å	A	100.0% 1-292	PDBe RCSB PDBj File	Viewing
AlphaFold PA2887	AlphaFold	—	—	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				0.443
6				0.343

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	6.5	0.328
2	2.68	0.079
3	1.57	0.024
4	1.51	0.022

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				0.703

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.

45 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
AAE	6ZZQ	A0A1E3M3N6	102.1 Da LogP 0.05 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CC(=O)O`
ADE	1YXM	Q9BY49	135.1 Da LogP -0.06 TPSA 80.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)c(ncn2)N`
BTB	5JC8	Q13GE3	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
HXC	4FC6	Q9NUI1	865.7 Da LogP 0.25 TPSA 363.6	3 viol.	✓ Clean	`CCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@@…`
QT8	6ZZS	A0A1E3M3N6	116.1 Da LogP 0.44 TPSA 54.4	✓ Ro5	✓ Clean	`CCC(=O)CC(=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
KDH	Q8I2S7	6.50	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`c1c(cc(c(c1O)O)O)[C@@H]2[C@@H](Cc3c(cc(cc3O2)O)…`

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
ZINC1615342	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC3870412	1.000	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c…`
ZINC3870413	1.000	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(…`
ZINC3870414	1.000	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c(…`
ZINC3870415	1.000	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(O…`
ZINC14436185	0.854	472.4 Da LogP 2.54 TPSA 186.4	2 viol.	Alert	`COc1cc(C(=O)O[C@@H]2Cc3c(O)cc(O)cc3O[C@@H]2c2cc…`
ZINC3978503	0.851	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)c(O)…`
ZINC4534390	0.851	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)c(O)c…`
ZINC4544252	0.851	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1ccc(O)c(O)c1…`
ZINC8681494	0.851	442.4 Da LogP 2.53 TPSA 177.1	1 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1ccc(O)c(O)c…`
ZINC14727965	0.848	426.4 Da LogP 2.82 TPSA 156.9	1 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)cc1)…`
ZINC21992193	0.760	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c…`
ZINC21992196	0.760	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c(…`
ZINC21992198	0.760	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(…`
ZINC21992201	0.760	458.4 Da LogP 2.23 TPSA 197.4	2 viol.	Alert	`O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(O…`
ZINC14642643	0.722	456.4 Da LogP 2.83 TPSA 166.1	1 viol.	Alert	`COc1cc(C(=O)O[C@@H]2Cc3c(O)cc(O)cc3O[C@@H]2c2cc…`
ZINC3870336	0.622	306.3 Da LogP 1.25 TPSA 130.6	1 viol.	Alert	`Oc1cc(O)c2c(c1)O[C@H](c1cc(O)c(O)c(O)c1)[C@H](O…`
ZINC3870337	0.622	306.3 Da LogP 1.25 TPSA 130.6	1 viol.	Alert	`Oc1cc(O)c2c(c1)O[C@@H](c1cc(O)c(O)c(O)c1)[C@H](…`
ZINC3870338	0.622	306.3 Da LogP 1.25 TPSA 130.6	1 viol.	Alert	`Oc1cc(O)c2c(c1)O[C@H](c1cc(O)c(O)c(O)c1)[C@@H](…`
ZINC3870339	0.622	306.3 Da LogP 1.25 TPSA 130.6	1 viol.	Alert	`Oc1cc(O)c2c(c1)O[C@@H](c1cc(O)c(O)c(O)c1)[C@@H]…`
ZINC43463386	0.533	261.0 Da LogP 0.54 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1nc(I)nc2[nH]cnc12`
ZINC4552271	0.533	237.5 Da LogP 2.18 TPSA 54.5	✓ Ro5	✓ Clean	`ClC(Cl)(Cl)c1ncnc2[nH]cnc12`
ZINC4707072	0.533	214.0 Da LogP 0.70 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1nc(Br)nc2[nH]cnc12`
ZINC12501123	0.522	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC4228234	0.522	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC79671662	0.522	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC79671663	0.522	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC2334905	0.522	261.4 Da LogP 1.10 TPSA 63.9	✓ Ro5	✓ Clean	`CC(C)CCN(CCC(C)C)C(CO)(CO)CO`
ZINC3159953	0.522	261.4 Da LogP 1.38 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCN(CCCCC)C(CO)(CO)CO`
ZINC14642853	0.517	442.4 Da LogP 2.18 TPSA 177.1	1 viol.	Alert	`O=C(Oc1cc(O)cc2c1C[C@H](O)[C@@H](c1ccc(O)c(O)c1…`
ZINC13610584	0.516	498.5 Da LogP 2.89 TPSA 177.1	1 viol.	Alert	`O=C(C[C@H](O)CCc1ccc(O)c(O)c1)O[C@@H]1Cc2c(O)cc…`
ZINC13610587	0.516	498.5 Da LogP 2.89 TPSA 177.1	1 viol.	Alert	`O=C(C[C@@H](O)CCc1ccc(O)c(O)c1)O[C@H]1Cc2c(O)cc…`
ZINC13610590	0.516	498.5 Da LogP 2.89 TPSA 177.1	1 viol.	Alert	`O=C(C[C@H](O)CCc1ccc(O)c(O)c1)O[C@H]1Cc2c(O)cc(…`
ZINC8652640	0.516	498.5 Da LogP 2.89 TPSA 177.1	1 viol.	Alert	`O=C(C[C@@H](O)CCc1ccc(O)c(O)c1)O[C@@H]1Cc2c(O)c…`
ZINC1560407548	0.500	441.4 Da LogP 2.69 TPSA 177.1	1 viol.	Alert	`O=C(O[C]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)c(O)c1)…`
ZINC5297554	0.500	289.5 Da LogP 2.16 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCN(CCCCCC)C(CO)(CO)CO`
ZINC5543260	0.500	200.2 Da LogP -0.40 TPSA 108.8	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ncnc2[nH]cnc12`
ZINC97941822	0.500	317.5 Da LogP 2.94 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCCN(CCCCCCC)C(CO)(CO)CO`
ZINC97942927	0.500	373.6 Da LogP 4.51 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCCCCN(CCCCCCCCC)C(CO)(CO)CO`

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.