Protein profile

PA5237

3-octaprenyl-4-hydroxybenzoate carboxy-lyase

Genome: NC_002516.2

Gene: PA5237 ubiD Structure source: AlphaFold UniProt Q9HTV3

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Amino acids 488

Annotations 8

Features 14

PDB binders 21

Druggability 0.741

Overview

Basic information about this protein and its source genome.

Accession: PA5237
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5237 ubiD
Status: annotated
Amino acids: 488
Structure source: AlphaFold

4.1.1.98

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0008694 Catalysis of the reaction: a 4-hydroxy-3-(all-trans-polyprenyl)benzoate + H+ = a 2-(all-trans-polyprenyl)phenol + CO2. GO:0046872 Binding to a metal ion. GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
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 0.741

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MTFKDLRDFIAQLEQRGALKRIQVPISPVLEMTEVCDRTLRAKGPALLFEKPTGFDMPVLGNLFGTPERVALGMGAEDVGALREIGKLLAQLKEPEPPKGLKDAWAKLPMYRKVLSMAPKVLKDAPCQEVVEEGEDVDLGRLPVQTCWPGDVGPLITWGLTVTRGPNKERQNLGIYRQQVIGRNKVIMRWLSHRGGALDYREWCQKHPGQPYPVAVALGADPATILGAVTPVPDTLSEYAFAGLLRGHRTELVKCRGSDLQVPASAEIVLEGVIHPGEMADEGPYGDHTGYYNEVDRFPVFTVERVTRRQKPIYHSTYTGRPPDEPAILGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRMAVVTMKKQYPGHAKRVMLGVWSFLRQFMYTKFVIVTDDDIDARDWNDVIWAITTRMDPKRDTVMIDNTPIDYLDFASPVSGLGSKMGLDATHKWPGETSREWGRAIVKDEAVTRRIDALWSSLGID

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

4.1.1.98

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0008694 Catalysis of the reaction: a 4-hydroxy-3-(all-trans-polyprenyl)benzoate + H+ = a 2-(all-trans-polyprenyl)phenol + CO2.
GO:0046872 Binding to a metal ion.
GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
10	431	Pfam	PF01977	3-octaprenyl-4-hydroxybenzoate carboxy-lyase
10	431	InterPro	IPR002830	UbiD decarboxylyase family
6	455	NCBIfam	TIGR00148	UbiD family decarboxylase
6	455	InterPro	IPR002830	UbiD decarboxylyase family
323	487	SUPERFAMILY	SSF143968	UbiD C-terminal domain-like
1	486	PANTHER	PTHR30108	3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE-RELATED
1	486	InterPro	IPR002830	UbiD decarboxylyase family
455	488	Gene3D	G3DSA:1.20.5.570	Single helix bin
455	488	FunFam	G3DSA:1.20.5.570:FF:000001	3-octaprenyl-4-hydroxybenzoate carboxy-lyase
1	487	Hamap	MF_01636	3-octaprenyl-4-hydroxybenzoate carboxy-lyase [ubiD].
1	487	InterPro	IPR023677	UbiD decarboxylyase, bacteria
337	453	Gene3D	G3DSA:3.40.1670.10	-
337	454	FunFam	G3DSA:3.40.1670.10:FF:000001	3-octaprenyl-4-hydroxybenzoate carboxy-lyase
3	322	SUPERFAMILY	SSF50475	FMN-binding split barrel

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 PA5237	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				0.741
1				0.731

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.

71 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
4LU	4ZA4	A2QHE5	525.5 Da LogP -0.09 TPSA 199.4	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(CC=[N+]3C4=C(N2C[C@@H]([C@@H]([…`
4LV	4ZA7	A2QHE5	162.2 Da LogP 2.17 TPSA 37.3	✓ Ro5	✓ Clean	`C/C(=C\c1ccccc1)/C(=O)O`
4LW	6R2R	A2QHE5	166.2 Da LogP 2.08 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)/C=C(/C(=O)O)\F`
4M4	4ZAA	A2QHE5	150.2 Da LogP 2.04 TPSA 29.5	✓ Ro5	✓ Clean	`COc1cc(ccc1O)C=C`
4MJ	4ZA9	A2QHE5	644.6 Da LogP 1.32 TPSA 216.7	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H](…`
7D9	5M1E	P0AAB5	606.5 Da LogP -0.64 TPSA 254.0	3 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H](…`
BYN	6EVD	A2QHE5	542.5 Da LogP -0.13 TPSA 220.1	3 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H](…`
CO2	4ZAA	A2QHE5	44.0 Da LogP -0.58 TPSA 34.1	✓ Ro5	✓ Clean	`C(=O)=O`
F5C	4ZA8	A2QHE5	238.1 Da LogP 2.48 TPSA 37.3	✓ Ro5	✓ Clean	`C(=C/C(=O)O)\c1c(c(c(c(c1F)F)F)F)F`
FZZ	4ZA5	A2QHE5	524.5 Da LogP 0.54 TPSA 209.0	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(CC3=NC4=C(N2C[C@@H]([C@@H]([C@@…`
JQ8	6R2T	A2QHE5	146.1 Da LogP 1.12 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)C#CC(=O)O`
JQH	6R33	A2QHE5	626.6 Da LogP 1.66 TPSA 192.5	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(C[C@@H]4[N@]3[C@]5(C(=C4)c6cccc…`
JQK	6R3F	A2QHE5	630.6 Da LogP 2.56 TPSA 199.9	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H](…`
JQQ	6R3G	A2QHE5	648.6 Da LogP 2.50 TPSA 199.9	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(C[C@H](N3C4=C(N2C[C@@H]([C@@H](…`
JQZ	6R32	A2QHE5	—	—	—	`CC1=CC2=[N](C3=C4(C(=C([C@H]5[N]4=C2C(=C1C)C(C5…`
JRH	6R3J	A2QHE5	566.5 Da LogP 0.60 TPSA 192.5	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(C[C@@H]4[N@]3[C@]5([C@@H](C4)C)…`
JRK	6R3N	A2QHE5	608.5 Da LogP -0.03 TPSA 229.8	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(C[C@@H]4[N@]3[C@]5(C(=C4C(=O)O)…`
JRN	6R3I	A2QHE5	720.6 Da LogP 1.30 TPSA 200.9	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(C[C@H]([n+]3c4c([n+]2C[C@@H]([C…`
JSH	6R3L	A2QHE5	628.6 Da LogP 1.75 TPSA 192.5	2 viol.	✓ Clean	`Cc1cc2c3c(c1C)C(C[C@@H]4[N@]3[C@]5([C@@H](C4)c6…`
SYN	6R3L	A2QHE5	104.2 Da LogP 2.33 TPSA 0.0	✓ Ro5	✓ Clean	`C=Cc1ccccc1`
TCA	6R2P	A2QHE5	148.2 Da LogP 1.78 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)\C=C\C(=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
ZINC12342729	1.000	238.1 Da LogP 2.48 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)/C=C/c1c(F)c(F)c(F)c(F)c1F`
ZINC4481119	1.000	238.1 Da LogP 2.48 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)/C=C\c1c(F)c(F)c(F)c(F)c1F`
ZINC16951469	0.800	218.2 Da LogP 1.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)/C=C\c1ccc(/C=C\C(=O)O)cc1`
ZINC1857742971	0.800	218.2 Da LogP 1.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)C=Cc1ccc(C=CC(=O)O)cc1`
ZINC225518	0.800	218.2 Da LogP 1.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)/C=C/c1ccc(/C=C/C(=O)O)cc1`
ZINC4972290	0.800	218.2 Da LogP 1.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)/C=C\c1ccc(/C=C/C(=O)O)cc1`
ZINC153711	0.750	224.3 Da LogP 3.45 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)/C=C/c1ccc(-c2ccccc2)cc1`
ZINC20232541	0.750	224.3 Da LogP 3.45 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)/C=C\c1ccc(-c2ccccc2)cc1`
ZINC2053466799	0.750	224.3 Da LogP 3.45 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)C=Cc1ccc(-c2ccccc2)cc1`
ZINC5282356	0.750	262.4 Da LogP 4.76 TPSA 17.1	✓ Ro5	✓ Clean	`C/C(=C\c1ccccc1)C(=O)/C(C)=C/c1ccccc1`
ZINC2053483728	0.739	218.2 Da LogP 1.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)C=Cc1cccc(C=CC(=O)O)c1`
ZINC242770	0.739	218.2 Da LogP 1.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)/C=C/c1cccc(/C=C/C(=O)O)c1`
ZINC6191548	0.739	218.2 Da LogP 1.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)/C=C\c1cccc(/C=C/C(=O)O)c1`
ZINC6191549	0.739	218.2 Da LogP 1.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)/C=C\c1cccc(/C=C\C(=O)O)c1`
ZINC84496209	0.739	222.2 Da LogP 2.79 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)C#Cc1ccc(-c2ccccc2)cc1`
ZINC12358705	0.727	234.3 Da LogP 3.98 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(C=Cc1ccccc1)C=Cc1ccccc1`
ZINC1504183	0.727	234.3 Da LogP 3.98 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(/C=C/c1ccccc1)/C=C/c1ccccc1`
ZINC16991034	0.727	262.3 Da LogP 3.55 TPSA 34.1	✓ Ro5	Alert	`O=C(/C=C/c1ccccc1)C(=O)/C=C/c1ccccc1`
ZINC1857524274	0.727	234.3 Da LogP 3.98 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(C=Cc1ccccc1)/C=C\c1ccccc1`
ZINC29786395	0.727	234.3 Da LogP 3.98 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(/C=C\c1ccccc1)/C=C\c1ccccc1`
ZINC31636707	0.727	262.3 Da LogP 3.55 TPSA 34.1	✓ Ro5	Alert	`O=C(/C=C\c1ccccc1)C(=O)/C=C\c1ccccc1`
ZINC3844946	0.727	214.2 Da LogP 0.56 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)C#Cc1cccc(C#CC(=O)O)c1`
ZINC4721555	0.727	262.3 Da LogP 3.55 TPSA 34.1	✓ Ro5	Alert	`O=C(/C=C\c1ccccc1)C(=O)/C=C/c1ccccc1`
ZINC5014573	0.727	234.3 Da LogP 3.98 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(/C=C\c1ccccc1)/C=C/c1ccccc1`
ZINC185070	0.714	272.3 Da LogP 3.29 TPSA 58.9	✓ Ro5	✓ Clean	`COc1cc(/C=C/c2ccc(O)c(OC)c2)ccc1O`
ZINC3184478	0.714	230.3 Da LogP 2.66 TPSA 17.1	✓ Ro5	Alert	`O=C(C#Cc1ccccc1)C#Cc1ccccc1`
ZINC34530182	0.696	294.3 Da LogP 3.55 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)/C=C/c1ccc(-c2ccc(/C=C/C(=O)O)cc2)cc1`
ZINC44201139	0.680	220.1 Da LogP 2.34 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)/C=C/c1c(F)c(F)cc(F)c1F`
ZINC1651125	0.667	276.3 Da LogP 3.94 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(/C=C/c1ccccc1)CC(=O)/C=C/c1ccccc1`
ZINC1857776708	0.667	224.3 Da LogP 3.45 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)C=Cc1cccc(-c2ccccc2)c1`
ZINC1927726910	0.667	288.1 Da LogP 2.78 TPSA 37.3	✓ Ro5	✓ Clean	`CC(=Cc1ccc(I)cc1)C(=O)O`
ZINC196664	0.667	250.1 Da LogP 2.35 TPSA 46.5	✓ Ro5	✓ Clean	`COc1c(F)c(F)c(/C=C/C(=O)O)c(F)c1F`
ZINC21950987	0.667	224.3 Da LogP 3.45 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)/C=C/c1cccc(-c2ccccc2)c1`
ZINC2577965	0.667	240.3 Da LogP 3.58 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)/C=C/c1ccc(Oc2ccccc2)cc1`
ZINC31872164	0.667	276.3 Da LogP 3.94 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(/C=C\c1ccccc1)CC(=O)/C=C\c1ccccc1`
ZINC31872166	0.667	276.3 Da LogP 3.94 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(/C=C\c1ccccc1)CC(=O)/C=C/c1ccccc1`
ZINC3848644	0.667	288.1 Da LogP 2.78 TPSA 37.3	✓ Ro5	✓ Clean	`C/C(=C/c1ccc(I)cc1)C(=O)O`
ZINC5045937	0.667	222.3 Da LogP 3.97 TPSA 17.1	✓ Ro5	✓ Clean	`C/C(=C/c1ccccc1)C(=O)c1ccccc1`
ZINC5203159	0.667	222.3 Da LogP 3.97 TPSA 17.1	✓ Ro5	✓ Clean	`C/C(=C\c1ccccc1)C(=O)c1ccccc1`
ZINC5479866	0.667	288.1 Da LogP 2.78 TPSA 37.3	✓ Ro5	✓ Clean	`C/C(=C\c1ccc(I)cc1)C(=O)O`
ZINC86722755	0.667	245.0 Da LogP 2.84 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)/C(F)=C/c1ccc(Br)cc1`
ZINC4529040	0.655	241.1 Da LogP 2.94 TPSA 37.3	✓ Ro5	✓ Clean	`C/C(=C\c1cccc(Br)c1)C(=O)O`
ZINC1635826	0.645	300.3 Da LogP 2.57 TPSA 83.6	✓ Ro5	Alert	`COc1cc(/C=N/N=C/c2ccc(O)c(OC)c2)ccc1O`
ZINC16997495	0.645	300.3 Da LogP 2.57 TPSA 83.6	✓ Ro5	Alert	`COc1cc(/C=N\N=C/c2ccc(O)c(OC)c2)ccc1O`
ZINC254438868	0.645	300.3 Da LogP 2.57 TPSA 83.6	✓ Ro5	Alert	`COc1cc(C=NN=Cc2ccc(O)c(OC)c2)ccc1O`
ZINC5022931	0.645	300.3 Da LogP 2.57 TPSA 83.6	✓ Ro5	Alert	`COc1cc(/C=N\N=C\c2ccc(O)c(OC)c2)ccc1O`
ZINC11976050	0.643	218.3 Da LogP 3.47 TPSA 37.3	✓ Ro5	✓ Clean	`C/C(=C\c1ccc(C(C)(C)C)cc1)C(=O)O`
ZINC12349443	0.640	208.3 Da LogP 3.58 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(/C=C\c1ccccc1)c1ccccc1`
ZINC1857775681	0.640	227.1 Da LogP 2.55 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)C=Cc1ccc(Br)cc1`
ZINC1951348006	0.640	274.1 Da LogP 2.39 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)C=Cc1ccc(I)cc1`

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.