Protein profile

VK055_4498

S-ribosylhomocysteine lyase

Genome: KpATCC43816

Gene: luxS AIK83036.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GX56

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Amino acids 147

Annotations 5

Features 18

PDB binders 0

Druggability 0.448

Overview

Basic information about this protein and its source genome.

Accession: VK055_4498
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: luxS AIK83036.1
Status: annotated
Amino acids: 147
Structure source: AlphaFold + ColabFold

4.4.1.21

GO:0005506 Binding to an iron (Fe) ion. GO:0043768 Catalysis of the reaction: S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine. GO:0009372 The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms. 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): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.14

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 0.448

Structure A0A0H3GX56

Pocket Pocket 1

P2Rank 0.049

Structure A0A0H3GX56

Pocket Pocket 1

ColabFold model

FPocket 0.258 · Pocket 1

P2Rank 0.075 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 205 / 4744 genomes with a hit

Normalized 0.043

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

4.4.1.21

Gene Ontology (GO)

GO:0005506 Binding to an iron (Fe) ion.
GO:0043768 Catalysis of the reaction: S-(5-deoxy-D-ribos-5-yl)-L-homocysteine = (S)-4,5-dihydroxypentane-2,3-dione + L-homocysteine.
GO:0009372 The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.
GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
53	71	PRINTS	PR01487	Bacterial autoinducer-2 (AI-2) production protein LuxS signature
53	71	InterPro	IPR003815	S-ribosylhomocysteinase (LuxS)
4	22	PRINTS	PR01487	Bacterial autoinducer-2 (AI-2) production protein LuxS signature
4	22	InterPro	IPR003815	S-ribosylhomocysteinase (LuxS)
97	116	PRINTS	PR01487	Bacterial autoinducer-2 (AI-2) production protein LuxS signature
97	116	InterPro	IPR003815	S-ribosylhomocysteinase (LuxS)
25	43	PRINTS	PR01487	Bacterial autoinducer-2 (AI-2) production protein LuxS signature
25	43	InterPro	IPR003815	S-ribosylhomocysteinase (LuxS)
1	147	Gene3D	G3DSA:3.30.1360.80	-
1	147	InterPro	IPR037005	S-ribosylhomocysteinase (LuxS) superfamily
2	128	Pfam	PF02664	S-Ribosylhomocysteinase (LuxS)
2	128	InterPro	IPR003815	S-ribosylhomocysteinase (LuxS)
1	138	SUPERFAMILY	SSF63411	LuxS/MPP-like metallohydrolase
1	138	InterPro	IPR011249	Metalloenzyme, LuxS/M16 peptidase-like
1	138	PIRSF	PIRSF006160	AI2
1	138	InterPro	IPR003815	S-ribosylhomocysteinase (LuxS)
1	135	PANTHER	PTHR35799	S-RIBOSYLHOMOCYSTEINE LYASE
1	135	InterPro	IPR003815	S-ribosylhomocysteinase (LuxS)

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_A0A0H3GX56	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_4498	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				0.448
2				0.002
4				0.002
3				0.0

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				2.34	0.049

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				0.258
7				0.001
5				0.0

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				2.92	0.075
2				2.23	0.045

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.

57 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.

No PDB ligands found through similar proteins.

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL208091	O34667	6.43	268.3 Da LogP -2.25 TPSA 153.1	1 viol.	✓ Clean	`N[C@@H](CCSC[C@H](O)[C@@H](O)C(=O)NO)C(=O)O`
CHEMBL593446	O34667	6.37	267.3 Da LogP -2.04 TPSA 133.2	✓ Ro5	✓ Clean	`N[C@@H](CCSC[C@H]1OC(O)[C@H](O)[C@@H]1O)C(=O)O`
CHEMBL595659	O34667	6.16	269.3 Da LogP -1.06 TPSA 113.0	✓ Ro5	✓ Clean	`N[C@@H](CCSC[C@H]1OC(O)[C@H](O)[C@@H]1F)C(=O)O`
CHEMBL207406	O34667	6.14	268.3 Da LogP -2.25 TPSA 153.1	1 viol.	✓ Clean	`N[C@@H](CCSC[C@@H](O)[C@@H](O)C(=O)NO)C(=O)O`
CHEMBL1078480	P45578	—	310.0 Da LogP 3.62 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCC1=CC(=C(Br)Br)OC1=O`
CHEMBL1078481	P45578	—	253.9 Da LogP 2.06 TPSA 26.3	✓ Ro5	✓ Clean	`O=C1C=CC(=C(Br)Br)O1`
CHEMBL448241	P45578	—	310.0 Da LogP 3.62 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCC1=C(Br)/C(=C/Br)OC1=O`

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
ZINC1762530	1.000	253.9 Da LogP 2.06 TPSA 26.3	✓ Ro5	✓ Clean	`O=C1C=CC(=C(Br)Br)O1`
ZINC1674993	0.640	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSCCSCC[C@H](N)C(=O)O)C(=O)O`
ZINC1674994	0.640	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSCCSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1674996	0.640	296.4 Da LogP 0.06 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCSCCSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1529407	0.615	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSC[C@@H](N)C(=O)O)C(=O)O`
ZINC1532680	0.615	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCSC[C@H](N)C(=O)O)C(=O)O`
ZINC1708208	0.615	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CSCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1605257	0.613	280.4 Da LogP 0.39 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CCSC)C(=O)O`
ZINC1605258	0.613	280.4 Da LogP 0.39 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@H](N)CCSC)C(=O)O`
ZINC1605259	0.613	280.4 Da LogP 0.39 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@H](CCSC)C(=O)O`
ZINC1605260	0.613	280.4 Da LogP 0.39 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)N[C@H](CCSC)C(=O)O`
ZINC2384801	0.613	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](C)C(=O)O`
ZINC4556875	0.613	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)N[C@@H](C)C(=O)O`
ZINC4556876	0.613	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)N[C@H](C)C(=O)O`
ZINC4556877	0.613	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@H](C)C(=O)O`
ZINC1708207	0.606	222.3 Da LogP -1.07 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCSC[C@H](N)C(=O)O)C(=O)O`
ZINC1569523	0.581	206.3 Da LogP -0.73 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)NCC(=O)O`
ZINC1593212	0.581	206.3 Da LogP -0.73 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)NCC(=O)O`
ZINC2384813	0.576	236.3 Da LogP -1.37 TPSA 112.7	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CO)C(=O)O`
ZINC2384835	0.576	264.3 Da LogP -0.89 TPSA 129.7	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC2390943	0.576	248.3 Da LogP 0.29 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC4557150	0.576	236.3 Da LogP -1.37 TPSA 112.7	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@H](CO)C(=O)O`
ZINC4899465	0.576	411.6 Da LogP 0.63 TPSA 121.5	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CCSC)C(=O)N[C@@H](CCSC…`
ZINC64219373	0.576	411.6 Da LogP 0.63 TPSA 121.5	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CCSC)C(=O)N[C@H](CCSC)…`
ZINC11755051	0.567	204.3 Da LogP 0.94 TPSA 46.3	✓ Ro5	✓ Clean	`CCN(CC)C(=O)[C@@H](N)CCSC`
ZINC57358674	0.567	205.3 Da LogP 1.41 TPSA 52.3	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)OC(C)(C)C`
ZINC57933694	0.567	205.3 Da LogP 1.41 TPSA 52.3	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)OC(C)(C)C`
ZINC62725402	0.567	204.3 Da LogP 0.94 TPSA 46.3	✓ Ro5	✓ Clean	`CCN(CC)C(=O)[C@H](N)CCSC`
ZINC2522690	0.563	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)NCCC(=O)O`
ZINC1698833	0.552	203.2 Da LogP 1.04 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](CCSC(F)(F)F)C(=O)O`
ZINC2041757	0.552	203.2 Da LogP 1.04 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](CCSC(F)(F)F)C(=O)O`
ZINC1576323	0.543	263.3 Da LogP -1.49 TPSA 135.5	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CC(N)=O)C(=O)O`
ZINC1576325	0.543	263.3 Da LogP -1.49 TPSA 135.5	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@H](CC(N)=O)C(=O)O`
ZINC2390945	0.543	262.4 Da LogP 0.68 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)O`
ZINC2516118	0.543	278.3 Da LogP -0.50 TPSA 129.7	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC4557160	0.543	262.4 Da LogP 0.68 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)N[C@@H](CC(C)C)C(=O)O`
ZINC4557161	0.543	262.4 Da LogP 0.68 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)N[C@H](CC(C)C)C(=O)O`
ZINC4557162	0.543	262.4 Da LogP 0.68 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@H](CC(C)C)C(=O)O`
ZINC3055005	0.542	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.542	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.542	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC106506744	0.531	303.5 Da LogP 4.44 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCSCC[C@H](N)C(=O)O`
ZINC11754909	0.531	204.3 Da LogP 0.84 TPSA 55.1	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)NCC(C)C`
ZINC11754910	0.531	202.3 Da LogP 0.69 TPSA 46.3	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N1CCCC1`
ZINC1757778	0.531	222.3 Da LogP 0.37 TPSA 66.6	✓ Ro5	✓ Clean	`CN(C)C(=S)SCC[C@H](N)C(=O)O`
ZINC2033572	0.531	222.3 Da LogP 0.37 TPSA 66.6	✓ Ro5	✓ Clean	`CN(C)C(=S)SCC[C@@H](N)C(=O)O`
ZINC34175843	0.531	202.3 Da LogP 0.69 TPSA 46.3	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)N1CCCC1`
ZINC62725431	0.531	204.3 Da LogP 0.84 TPSA 55.1	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)NCC(C)C`
ZINC62725433	0.531	204.3 Da LogP 0.98 TPSA 55.1	✓ Ro5	✓ Clean	`CC[C@@H](C)NC(=O)[C@H](N)CCSC`
ZINC62725435	0.531	204.3 Da LogP 0.98 TPSA 55.1	✓ Ro5	✓ Clean	`CC[C@H](C)NC(=O)[C@H](N)CCSC`

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.