Protein profile

PA5387

carnitine dehydrogenase

Genome: NC_002516.2

Gene: cdhC PA5387 Structure source: AlphaFold UniProt Q9HTH7

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Amino acids 294

Annotations 4

Features 7

PDB binders 4

Druggability 0.573

Overview

Basic information about this protein and its source genome.

Accession: PA5387
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: cdhC PA5387
Status: annotated
Amino acids: 294
Structure source: AlphaFold

2.3.1.317

GO:0043720 Catalysis of the reaction: 3-keto-5-aminohexanoate + acetyl-CoA = L-3-aminobutyryl-CoA + acetoacetate. GO:0046872 Binding to a metal ion. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
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 0.573

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

2.3.1.317

Gene Ontology (GO)

GO:0043720 Catalysis of the reaction: 3-keto-5-aminohexanoate + acetyl-CoA = L-3-aminobutyryl-CoA + acetoacetate.
GO:0046872 Binding to a metal ion.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

7 records

Show feature table

Start	End	DB	Term	Name
2	294	Gene3D	G3DSA:3.20.20.70	Aldolase class I
2	294	InterPro	IPR013785	Aldolase-type TIM barrel
1	293	PANTHER	PTHR37418	3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME-RELATED
1	293	InterPro	IPR008567	Beta-keto acid cleavage enzymes
2	294	FunFam	G3DSA:3.20.20.70:FF:000224	3-keto-5-aminohexanoate cleavage enzyme
5	291	Pfam	PF05853	beta-keto acid cleavage enzyme
5	291	InterPro	IPR008567	Beta-keto acid cleavage enzymes

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 PA5387	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				0.573

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.

46 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	2Y7G	B0VHH0	102.1 Da LogP 0.05 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CC(=O)O`
ETX	3E49	Q13GE9	90.1 Da LogP 0.02 TPSA 29.5	✓ Ro5	✓ Clean	`CCOCCO`
KMH	2Y7F	B0VHH0	145.2 Da LogP -0.23 TPSA 80.4	✓ Ro5	✓ Clean	`C[C@@H](CC(=O)CC(=O)O)N`
TAR	5ZMY	F1LJ99	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).

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
ZINC5650743	0.875	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	0.875	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC12359024	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
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`
ZINC12501520	0.563	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	0.563	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.563	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.563	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	0.563	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.563	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5859031	0.563	294.4 Da LogP 1.13 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCC`
ZINC3780929	0.526	382.5 Da LogP 4.10 TPSA 36.9	✓ Ro5	✓ Clean	`CCOCCP(CCOCC)CCP(CCOCC)CCOCC`
ZINC1644613	0.524	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC1529331	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@H](C(=O)O)[C@@H](O)C(=O)O`
ZINC1529332	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@H](C(=O)O)[C@H](O)C(=O)O`
ZINC1529333	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@@H](C(=O)O)[C@@H](O)C(=O)O`
ZINC1529334	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@@H](C(=O)O)[C@H](O)C(=O)O`
ZINC1580159	0.500	210.3 Da LogP -0.26 TPSA 58.9	✓ Ro5	✓ Clean	`OCCOCCSCCOCCO`
ZINC1580161	0.500	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.500	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.500	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1849711	0.500	202.3 Da LogP 3.14 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCO`
ZINC1850542	0.500	216.4 Da LogP 3.53 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCO`
ZINC2173592	0.500	216.4 Da LogP 3.79 TPSA 18.5	✓ Ro5	✓ Clean	`CCOCCCCCCCCCOCC`
ZINC2555269	0.500	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC28278447	0.500	230.4 Da LogP 4.18 TPSA 18.5	✓ Ro5	✓ Clean	`CCOCCCCCCCCCCOCC`
ZINC34317654	0.500	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	0.500	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.500	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC59660505	0.500	244.4 Da LogP 4.31 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCO`
ZINC5997860	0.500	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC8437287	0.500	230.4 Da LogP 3.92 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCO`
ZINC85733754	0.500	258.4 Da LogP 4.70 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCO`

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.