Protein profile

KP13_01739

3-octaprenyl-4-hydroxybenzoate carboxy-lyase

Genome: KpKP13

Gene: AHE46958.1 ubiD Structure source: AlphaFold + ColabFold UniProt A0A0H3GKH2

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Amino acids 491

Annotations 7

Features 14

PDB binders 22

Druggability 0.578

Overview

Basic information about this protein and its source genome.

Accession: KP13_01739
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46958.1 ubiD
Status: annotated
Amino acids: 491
Structure source: AlphaFold + ColabFold

4.1.1.98

GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound. 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:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 96.122
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 93.47

Selected Druggability evidence

AlphaFold / UniProt model

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 0.578

Structure A0A0H3GKH2

Pocket Pocket 17

P2Rank 0.869

Structure A0A0H3GKH2

Pocket Pocket 1

ColabFold model

FPocket 0.163 · Pocket 7

P2Rank 0.872 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 157 / 4744 genomes with a hit

Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

4.1.1.98

Gene Ontology (GO)

GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
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:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
455	491	Gene3D	G3DSA:1.20.5.570	Single helix bin
337	454	FunFam	G3DSA:3.40.1670.10:FF:000001	3-octaprenyl-4-hydroxybenzoate carboxy-lyase
11	431	Pfam	PF01977	3-octaprenyl-4-hydroxybenzoate carboxy-lyase
11	431	InterPro	IPR002830	UbiD decarboxylyase family
3	322	SUPERFAMILY	SSF50475	FMN-binding split barrel
1	487	Hamap	MF_01636	3-octaprenyl-4-hydroxybenzoate carboxy-lyase [ubiD].
1	487	InterPro	IPR023677	UbiD decarboxylyase, bacteria
1	485	PANTHER	PTHR30108	3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE-RELATED
1	485	InterPro	IPR002830	UbiD decarboxylyase family
337	454	Gene3D	G3DSA:3.40.1670.10	-
6	455	NCBIfam	TIGR00148	UbiD family decarboxylase
6	455	InterPro	IPR002830	UbiD decarboxylyase family
455	491	FunFam	G3DSA:1.20.5.570:FF:000001	3-octaprenyl-4-hydroxybenzoate carboxy-lyase
323	486	SUPERFAMILY	SSF143968	UbiD C-terminal domain-like

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 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GKH2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01739	ColabFold	—	—	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
17				0.578
7				0.343
1				0.004
12				0.001

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	25.87	0.869
2	7.0	0.303
3	2.43	0.053
4	2.08	0.039
5	1.82	0.029

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
7				0.163
2				0.029
9				0.002
35				0.002

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	26.31	0.872
2	4.72	0.171
3	2.53	0.057
4	2.37	0.051
5	1.68	0.024

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.

72 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	5M1D	P0AAB4	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](…`
4VP	4S13	Q03034	120.2 Da LogP 2.04 TPSA 20.2	✓ Ro5	✓ Clean	`C=Cc1ccc(cc1)O`
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`
ZINC20231841	0.640	274.1 Da LogP 2.39 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)/C=C\c1ccc(I)cc1`
ZINC38139289	0.640	208.3 Da LogP 3.58 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(/C=C/c1ccccc1)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.