Protein profile

VK055_3046

chorismate lyase

Genome: KpATCC43816

Gene: AIK81631.1 ubiC Structure source: AlphaFold + ColabFold UniProt A0A0H3GGV2

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Amino acids 165

Annotations 6

Features 11

PDB binders 2

Druggability 0.91

Overview

Basic information about this protein and its source genome.

Accession: VK055_3046
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK81631.1 ubiC
Status: annotated
Amino acids: 165
Structure source: AlphaFold + ColabFold

4.1.3.40

GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme. GO:0008813 Catalysis of the reaction: chorismate = 4-hydroxybenzoate + pyruvate. 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:0042866 The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate.

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 (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 92.42

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 0.91

Structure A0A0H3GGV2

Pocket Pocket 1

P2Rank 0.667

Structure A0A0H3GGV2

Pocket Pocket 1

ColabFold model

FPocket 0.931 · Pocket 1

P2Rank 0.544 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 112 / 4744 genomes with a hit

Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

4.1.3.40

Gene Ontology (GO)

GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
GO:0008813 Catalysis of the reaction: chorismate = 4-hydroxybenzoate + pyruvate.
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:0042866 The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
2	165	Gene3D	G3DSA:3.40.1410.10	-
2	165	InterPro	IPR028978	Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily
1	165	PANTHER	PTHR38683	CHORISMATE PYRUVATE-LYASE
1	165	InterPro	IPR007440	Chorismate--pyruvate lyase
8	165	SUPERFAMILY	SSF64288	Chorismate lyase-like
8	165	InterPro	IPR028978	Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily
12	165	Hamap	MF_01632	Chorismate pyruvate-lyase [ubiC].
12	165	InterPro	IPR007440	Chorismate--pyruvate lyase
2	165	FunFam	G3DSA:3.40.1410.10:FF:000002	Chorismate pyruvate-lyase
18	165	Pfam	PF04345	Chorismate lyase
18	165	InterPro	IPR007440	Chorismate--pyruvate lyase

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_A0A0H3GGV2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3046	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				0.91

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				7.39	0.387
2				0.73	0.002

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				0.931

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				5.57	0.267

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.

52 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
PHB	1FW9	P26602	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)O)O`
VNL	1XLR	P26602	167.1 Da LogP -0.24 TPSA 69.6	✓ Ro5	✓ Clean	`COc1cc(ccc1O)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
ZINC389804	0.842	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(O)cc2)cc1`
ZINC1747299	0.750	302.3 Da LogP 2.18 TPSA 93.1	✓ Ro5	Alert	`COc1cc(C(=O)C(=O)c2ccc(O)c(OC)c2)ccc1O`
ZINC33246180	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(O)cc2)cc1`
ZINC3896282	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccc(O)cc2)cc1`
ZINC392302	0.727	230.2 Da LogP 2.88 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(O)cc2)cc1`
ZINC289893	0.696	278.3 Da LogP 1.92 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)c2ccc(O)cc2)cc1`
ZINC1595860	0.677	316.3 Da LogP 2.48 TPSA 82.1	✓ Ro5	Alert	`COc1cc(C(=O)C(=O)c2ccc(OC)c(OC)c2)ccc1O`
ZINC114185151	0.667	298.2 Da LogP 2.15 TPSA 108.7	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC2924369	0.667	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccc(O)cc1`
ZINC103291148	0.656	356.4 Da LogP 3.52 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(C(=O)/C(C)=C(/C)C(=O)c2ccc(O)c(OC)c2)ccc…`
ZINC3156317	0.640	258.2 Da LogP 2.31 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccc(O)cc2)cc1`
ZINC4903179	0.640	257.2 Da LogP 2.34 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2ccc(O)cc2)cc1`
ZINC134079	0.632	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1640789	0.632	374.3 Da LogP 3.55 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)c3ccc(C(=O)O)cc3)cc…`
ZINC2146859	0.632	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC28449	0.632	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(O)cc1`
ZINC3147211	0.632	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC332365	0.632	318.3 Da LogP 3.56 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(C(=O)c2ccc(O)cc2)cc1`
ZINC1705144	0.619	226.2 Da LogP 2.46 TPSA 54.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccccc1`
ZINC1747330	0.618	362.3 Da LogP 2.13 TPSA 111.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)OCCOC(=O)c2ccc(O)c(OC)c2)ccc1O`
ZINC38237511	0.618	242.3 Da LogP 2.94 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)c2ccc(C)cc2)ccc1O`
ZINC49181262	0.600	372.4 Da LogP 2.73 TPSA 105.6	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@]2(C)O[C@@]2(C)C(=O)c2ccc(O)c(O…`
ZINC49181265	0.600	372.4 Da LogP 2.73 TPSA 105.6	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@]2(C)O[C@]2(C)C(=O)c2ccc(O)c(OC…`
ZINC49181268	0.600	372.4 Da LogP 2.73 TPSA 105.6	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@]2(C)O[C@@]2(C)C(=O)c2ccc(O)c(OC…`
ZINC6338454	0.593	268.3 Da LogP 2.99 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/C(=O)c2ccc(O)cc2)cc1`
ZINC1747304	0.583	288.3 Da LogP 2.54 TPSA 76.0	✓ Ro5	✓ Clean	`COc1cc(CC(=O)c2ccc(O)c(OC)c2)ccc1O`
ZINC266	0.583	223.3 Da LogP 1.88 TPSA 49.8	✓ Ro5	✓ Clean	`CCN(CC)C(=O)c1ccc(O)c(OC)c1`
ZINC36108805	0.583	224.2 Da LogP 1.45 TPSA 83.8	✓ Ro5	✓ Clean	`COc1cc(C(=O)CCC(=O)O)ccc1O`
ZINC65340137	0.583	258.2 Da LogP 2.46 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)cc(-c2ccc(O)cc2)c1`
ZINC167246	0.571	248.0 Da LogP 1.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)cc1`
ZINC3269660	0.571	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC34573580	0.571	496.5 Da LogP 4.86 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(c2ccc(C(=O)O)cc2)(c2ccc(C(=O)O)cc…`
ZINC388063	0.571	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Br)cc1`
ZINC65342513	0.571	244.2 Da LogP 2.77 TPSA 66.8	✓ Ro5	✓ Clean	`COc1cc(-c2ccc(C(=O)O)cc2)ccc1O`
ZINC13340359	0.568	212.2 Da LogP -0.06 TPSA 87.0	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@H](O)CO)ccc1O`
ZINC13340360	0.568	212.2 Da LogP -0.06 TPSA 87.0	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@H](O)CO)ccc1O`
ZINC1668317	0.568	210.2 Da LogP 1.97 TPSA 55.8	✓ Ro5	✓ Clean	`CCCOC(=O)c1ccc(O)c(OC)c1`
ZINC1747307	0.568	304.3 Da LogP 2.03 TPSA 96.2	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@H](O)c2ccc(O)c(OC)c2)ccc1O`
ZINC2042188	0.568	304.3 Da LogP 2.03 TPSA 96.2	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@H](O)c2ccc(O)c(OC)c2)ccc1O`
ZINC75616154	0.568	208.3 Da LogP 2.77 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCC(=O)c1ccc(O)c(OC)c1`
ZINC82722760	0.568	238.2 Da LogP 1.54 TPSA 72.8	✓ Ro5	✓ Clean	`COC(=O)CCC(=O)c1ccc(O)c(OC)c1`
ZINC1747263	0.553	224.3 Da LogP 2.21 TPSA 55.8	✓ Ro5	✓ Clean	`COc1cc(C(=O)OCC(C)C)ccc1O`
ZINC34133836	0.553	211.2 Da LogP 0.12 TPSA 78.8	✓ Ro5	✓ Clean	`COc1cc(C(=O)NCCO)ccc1O`
ZINC4792435	0.553	223.3 Da LogP 1.54 TPSA 49.8	✓ Ro5	✓ Clean	`COc1cc(C(=O)CCN(C)C)ccc1O`
ZINC5234593	0.552	293.3 Da LogP 1.89 TPSA 103.7	✓ Ro5	Alert	`O=C(O)c1ccc(S(=O)(=O)Nc2ccc(O)cc2)cc1`
ZINC156520	0.545	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/c2ccc(C(=O)O)cc2)cc1`
ZINC241160	0.545	258.2 Da LogP 2.88 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(C(=O)O)cc2)cc1`
ZINC2504355	0.545	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC4792283	0.545	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C\c2ccc(C(=O)O)cc2)cc1`
ZINC8418684	0.545	257.2 Da LogP 2.83 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Nc2ccc(C(=O)O)cc2)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.