Protein profile

PA5386

3-hydroxybutyryl-CoA dehydrogenase

Genome: NC_002516.2

Gene: cdhA PA5386 Structure source: AlphaFold UniProt Q9HTH8

Export view

Amino acids 321

Annotations 8

Features 18

PDB binders 8

Druggability 0.903

Overview

Basic information about this protein and its source genome.

Accession: PA5386
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: cdhA PA5386
Status: annotated
Amino acids: 321
Structure source: AlphaFold

1.1.1.108

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0047728 Catalysis of the reaction: carnitine + NAD+ = 3-dehydrocarnitine + H+ + NADH. GO:0070403 Binding to the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0042413 The chemical reactions and pathways resulting in the breakdown of carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane. GO:0006631 The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 40.458
Human E-value: 9.18e-25
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 0.903

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1.1.1.108

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0047728 Catalysis of the reaction: carnitine + NAD+ = 3-dehydrocarnitine + H+ + NADH.
GO:0070403 Binding to the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GO:0042413 The chemical reactions and pathways resulting in the breakdown of carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
GO:0006631 The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
189	310	Gene3D	G3DSA:1.10.1040.10	-
189	310	InterPro	IPR013328	6-phosphogluconate dehydrogenase, domain 2
8	318	Hamap	MF_02129	L-carnitine dehydrogenase [lcdH].
8	318	InterPro	IPR026578	L-carnitine dehydrogenase
188	275	SUPERFAMILY	SSF48179	6-phosphogluconate dehydrogenase C-terminal domain-like
188	275	InterPro	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
4	301	PIRSF	PIRSF000105	HCDH
4	301	InterPro	IPR022694	3-hydroxyacyl-CoA dehydrogenase
6	295	PANTHER	PTHR48075	3-HYDROXYACYL-COA DEHYDROGENASE FAMILY PROTEIN
6	185	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
6	185	InterPro	IPR036291	NAD(P)-binding domain superfamily
189	310	FunFam	G3DSA:1.10.1040.10:FF:000027	L-carnitine dehydrogenase
4	188	Gene3D	G3DSA:3.40.50.720	-
188	256	Pfam	PF00725	3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
188	256	InterPro	IPR006108	3-hydroxyacyl-CoA dehydrogenase, C-terminal
4	188	FunFam	G3DSA:3.40.50.720:FF:000522	L-carnitine dehydrogenase
11	184	Pfam	PF02737	3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
11	184	InterPro	IPR006176	3-hydroxyacyl-CoA dehydrogenase, NAD binding

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...

Legend High Medium Low

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 PA5386	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
2				0.428
5				0.246
1				0.221

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.

58 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
3H9	3ZWA	P07896	877.7 Da LogP -3.31 TPSA 395.2	3 viol.	✓ Clean	`CCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)…`
3HC	1F12	Q16836	853.6 Da LogP -1.56 TPSA 383.9	3 viol.	✓ Clean	`CC(CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](…`
CAA	4KUH	C4IEM5	851.6 Da LogP -1.36 TPSA 380.7	3 viol.	✓ Clean	`CC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P…`
HSC	3ZWC	P07896	933.8 Da LogP -1.75 TPSA 395.2	3 viol.	✓ Clean	`CCCCCCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C…`
N8E	1WDL	P28793	350.5 Da LogP 2.42 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCOCCO`
T1G	3ZW9	P07896	863.6 Da LogP -3.85 TPSA 395.2	3 viol.	✓ Clean	`C[C@@H]([C@H](C)O)C(=O)SCCNC(=O)CCNC(=O)[C@@H](…`
TC6	3ZWB	P07896	859.6 Da LogP -2.51 TPSA 374.9	2 viol.	✓ Clean	`CCC/C=C/C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP…`
ZOZ	5OMO	P07896	935.8 Da LogP 0.98 TPSA 380.7	3 viol.	✓ Clean	`CCCCCCCC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(…`

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
ZINC100014200	1.000	494.7 Da LogP 4.02 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC100070166	1.000	290.4 Da LogP 3.17 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCO`
ZINC100310628	1.000	478.7 Da LogP 4.78 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC100365196	1.000	302.5 Da LogP 4.71 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCO`
ZINC101772322	1.000	434.7 Da LogP 4.76 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC103600921	1.000	466.7 Da LogP 3.24 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC14880431	1.000	378.6 Da LogP 3.20 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC14881140	1.000	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
ZINC16051619	1.000	350.5 Da LogP 2.42 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCOCCO`
ZINC2584424	1.000	218.3 Da LogP 2.37 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCO`
ZINC4521877	1.000	234.3 Da LogP 1.61 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCO`
ZINC5273610	1.000	322.4 Da LogP 1.64 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCOCCOCCO`
ZINC58538366	1.000	392.6 Da LogP 3.59 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC58631420	1.000	422.6 Da LogP 3.22 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC59441819	1.000	318.5 Da LogP 3.95 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCO`
ZINC59622400	1.000	274.4 Da LogP 3.93 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCO`
ZINC71788551	1.000	334.5 Da LogP 3.19 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCO`
ZINC71788564	1.000	262.4 Da LogP 2.39 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCO`
ZINC71788567	1.000	406.6 Da LogP 3.98 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC8214594	1.000	362.6 Da LogP 3.97 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC88260008	1.000	390.6 Da LogP 4.75 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC95784968	1.000	450.7 Da LogP 4.00 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC95863931	1.000	464.7 Da LogP 4.39 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC1849711	0.950	202.3 Da LogP 3.14 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCO`
ZINC1850542	0.950	216.4 Da LogP 3.53 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCO`
ZINC2555269	0.950	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC59660505	0.950	244.4 Da LogP 4.31 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCO`
ZINC8437287	0.950	230.4 Da LogP 3.92 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCO`
ZINC85733754	0.950	258.4 Da LogP 4.70 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCO`
ZINC1644613	0.810	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC59545536	0.773	258.4 Da LogP 4.70 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCCO`
ZINC95831576	0.773	230.4 Da LogP 3.92 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCCCO`
ZINC1627284	0.700	214.4 Da LogP 4.94 TPSA 9.2	✓ Ro5	✓ Clean	`CCCCCCCOCCCCCCC`
ZINC2564179	0.700	214.4 Da LogP 4.94 TPSA 9.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCCCCC`
ZINC100302699	0.600	332.5 Da LogP 3.48 TPSA 65.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OCCOCCOCCO`
ZINC101013974	0.600	273.5 Da LogP 3.90 TPSA 44.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCN`
ZINC101367966	0.600	232.3 Da LogP 1.90 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OCCOCCO`
ZINC44583812	0.600	380.6 Da LogP 3.49 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCCCCCCCCCCS`
ZINC44583816	0.600	468.7 Da LogP 3.52 TPSA 75.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCCCCCCCCCCS`
ZINC6620298	0.600	336.5 Da LogP 3.47 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCCCCCCCCCCS`
ZINC86039630	0.600	288.4 Da LogP 3.46 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OCCOCCO`
ZINC100684628	0.586	330.6 Da LogP 4.77 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[N+](C)(C)CCOCCO`
ZINC4978403	0.583	248.4 Da LogP 2.00 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCCOCCCOCCCO`
ZINC100090646	0.571	448.6 Da LogP 4.86 TPSA 83.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCC(=O)O`
ZINC100645716	0.571	273.5 Da LogP 4.60 TPSA 35.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCC(N)=S`
ZINC100970335	0.571	331.5 Da LogP 3.44 TPSA 70.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCC(N)=O`
ZINC2041048	0.571	218.3 Da LogP 2.64 TPSA 27.7	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCCC`
ZINC1697133	0.565	214.4 Da LogP 4.94 TPSA 9.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCC`
ZINC5650743	0.565	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	0.565	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`

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.