Protein profile

VK055_1301

3-octaprenyl-4-hydroxybenzoate carboxy-lyase family protein

Genome: KpATCC43816

Gene: AIK79924.1 Structure source: Experimental + ColabFold UniProt A6T7M3

Export view

Amino acids 502

Annotations 1

Features 7

PDB binders 22

Druggability 0.858

Overview

Basic information about this protein and its source genome.

Accession: VK055_1301
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79924.1
Status: annotated
Amino acids: 502
Structure source: Experimental + ColabFold

GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 28.188
Localization: Cytoplasmic
ColabFold pLDDT: 94.91

Selected Druggability evidence

PDB experimental structure

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 0.858

Structure 5O3M

Pocket Pocket 1

P2Rank 0.826

Structure 5O3M

Pocket Pocket 1

ColabFold model

FPocket 0.446 · Pocket 12

P2Rank 0.888 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 406 / 4744 genomes with a hit

Normalized 0.086

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

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.

7 records

Show feature table

Start	End	DB	Term	Name
342	465	Gene3D	G3DSA:3.40.1670.10	-
4	478	PANTHER	PTHR30108	3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE-RELATED
4	478	InterPro	IPR002830	UbiD decarboxylyase family
18	433	Pfam	PF01977	3-octaprenyl-4-hydroxybenzoate carboxy-lyase
18	433	InterPro	IPR002830	UbiD decarboxylyase family
326	483	SUPERFAMILY	SSF143968	UbiD C-terminal domain-like
6	321	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...

Legend High Medium Low

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 5O3M	X-ray	20.00 Å	-	—	PDBe RCSB PDBj File	Viewing
ColabFold VK055_1301	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
1				0.463
151				0.411
66				0.214
20				0.208

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	22.45	0.881
2	18.64	0.826
3	17.84	0.809
4	17.68	0.806
5	15.93	0.766

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
12				0.446
28				0.394
27				0.389

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	16.04	0.768
2	5.1	0.233
3	1.27	0.013
4	0.87	0.003

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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
9JE	5O3M Open crystal	104.1 Da LogP 0.14 TPSA 40.5	✓ Ro5	✓ Clean	`C(CCO)CCO`

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`
ZINC14771652	1.000	216.4 Da LogP 3.26 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCO`
ZINC15269439	1.000	272.5 Da LogP 4.82 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCCCO`
ZINC1574339	1.000	202.3 Da LogP 2.87 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCO`
ZINC4202510	1.000	230.4 Da LogP 3.65 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCO`
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`
ZINC4521552	1.000	258.4 Da LogP 4.43 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCCO`
ZINC4600152	1.000	244.4 Da LogP 4.04 TPSA 40.5	✓ Ro5	✓ Clean	`OCCCCCCCCCCCCCCCO`
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`
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`
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`

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.