Protein profile

PA4053

6,7-dimethyl-8-ribityllumazine synthase

Genome: NC_002516.2

Gene: ribE PA4053 ribH Structure source: AlphaFold UniProt Q9HWX5

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Amino acids 158

Annotations 6

Features 15

PDB binders 12

Druggability 0.642

Overview

Basic information about this protein and its source genome.

Accession: PA4053
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: ribE PA4053 ribH
Status: annotated
Amino acids: 158
Structure source: AlphaFold

2.5.1.78

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:0009349 An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine. GO:0000906 Catalysis of the reaction: 3,4-dihydroxy-2-butanone-4-phosphate + 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione = 6,7-dimethyl-8-ribityllumazine + phosphate. GO:0009231 The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).

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 0.642

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MTLKTIEGTFIAPKGRYALVVGRFNSFVVESLVSGAVDALVRHGVAESEITIIRAPGAFEIPLVTQKVAQQGGFDAIIALGAVIRGGTPHFEYVAGECTKGLAQVSLQFGIPVAFGVLTVDSIEQAIERSGTKAGNKGAEAALSALEMVSLLAQLEAK

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

2.5.1.78

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:0009349 An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine.
GO:0000906 Catalysis of the reaction: 3,4-dihydroxy-2-butanone-4-phosphate + 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione = 6,7-dimethyl-8-ribityllumazine + phosphate.
GO:0009231 The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
10	155	Hamap	MF_00178	6,7-dimethyl-8-ribityllumazine synthase [ribH].
10	155	InterPro	IPR034964	Lumazine synthase
17	149	CDD	cd09209	Lumazine_synthase-I
17	149	InterPro	IPR034964	Lumazine synthase
15	157	PANTHER	PTHR21058	6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE DMRL SYNTHASE LUMAZINE SYNTHASE
15	157	InterPro	IPR034964	Lumazine synthase
3	157	Gene3D	G3DSA:3.40.50.960	Lumazine/riboflavin synthase
3	157	InterPro	IPR036467	Lumazine/riboflavin synthase superfamily
16	151	NCBIfam	TIGR00114	6,7-dimethyl-8-ribityllumazine synthase
16	151	InterPro	IPR034964	Lumazine synthase
16	152	Pfam	PF00885	6,7-dimethyl-8-ribityllumazine synthase
16	152	InterPro	IPR002180	Lumazine/riboflavin synthase
5	155	SUPERFAMILY	SSF52121	Lumazine synthase
5	155	InterPro	IPR036467	Lumazine/riboflavin synthase superfamily
3	157	FunFam	G3DSA:3.40.50.960:FF:000001	6,7-dimethyl-8-ribityllumazine synthase

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 PA4053	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
1				0.642

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.

69 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
5YL	1NQW	O66529	411.3 Da LogP -2.56 TPSA 216.2	1 viol.	✓ Clean	`C(CCC1=C(NC(=O)NC1=O)NC[C@@H]([C@@H]([C@@H](CO)…`
DLZ	4KQ6	Q6FXA8	326.3 Da LogP -2.88 TPSA 161.6	✓ Ro5	✓ Clean	`CC1=C(N(C2=NC(=O)NC(=O)C2=N1)C[C@@H]([C@@H]([C@…`
INI	1RVV	P11998	306.2 Da LogP -3.54 TPSA 201.8	1 viol.	✓ Clean	`C([C@@H]([C@@H]([C@@H](CO)O)O)O)NC1=C(C(=O)NC(=…`
JCL	2C97	P9WHE9	298.6 Da LogP 0.15 TPSA 132.5	✓ Ro5	✓ Clean	`C(CCOP(=O)(O)O)CC1=C(NC(=O)NC1=O)Cl`
LMZ	1NQV	O66529	290.2 Da LogP -3.05 TPSA 188.1	1 viol.	✓ Clean	`C([C@@H]([C@@H]([C@@H](CO)O)O)O)NC1=C(C(=O)NC(=…`
PHR	2C9D	P9WHE9	482.4 Da LogP -3.08 TPSA 240.3	2 viol.	✓ Clean	`C(CCCOP(=O)(O)O)CCN1C2=C(NC(=O)NC2=O)N(C1=O)C[C…`
PUG	2C9B	P9WHE9	302.2 Da LogP -4.22 TPSA 184.4	1 viol.	✓ Clean	`C([C@H]([C@@H]([C@@H](CO)O)O)O)N1C2=C(C(=O)NC(=…`
RDL	1NQU	O66529	330.3 Da LogP -4.86 TPSA 201.5	1 viol.	✓ Clean	`C([C@@H]([C@@H]([C@@H](CO)O)O)O)N1C2=C(C(=O)NC(…`
RLP	1NQX	O66529	386.3 Da LogP -3.77 TPSA 219.1	2 viol.	✓ Clean	`C(CC(=O)O)C1=C(N(C2=NC(=O)NC(=O)C2=N1)C[C@@H]([…`
TP6	2C92	P9WHE9	468.4 Da LogP -3.47 TPSA 240.3	2 viol.	✓ Clean	`C(CCN1C2=C(NC(=O)NC2=O)N(C1=O)C[C@H]([C@@H]([C@…`
TSF	2C94	P9WHE9	488.3 Da LogP -2.80 TPSA 231.1	1 viol.	✓ Clean	`C(CCN1C2=C(NC(=O)NC2=O)N(C1=O)C[C@H]([C@@H]([C@…`
Y19	2VI5	P9WHE9	332.3 Da LogP -3.81 TPSA 180.6	1 viol.	✓ Clean	`CCC(=O)N[C@@H]1C(=O)NC(=O)N=C1NC[C@@H]([C@@H]([…`

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
CHEMBL1095229	P9WHE9	—	261.6 Da LogP -0.78 TPSA 121.1	✓ Ro5	✓ Clean	`CCOC(=O)C(=O)Nc1c(Cl)[nH]c(=O)[nH]c1=O`
CHEMBL1095867	P9WHE9	—	428.4 Da LogP 2.35 TPSA 142.0	✓ Ro5	✓ Clean	`O=C1Nc2ccc(S(=O)(=O)NCCCCCCOP(=O)(O)O)c3cccc1c23`
CHEMBL1095991	P9WHE9	—	372.3 Da LogP 0.79 TPSA 142.0	✓ Ro5	✓ Clean	`O=C1Nc2ccc(S(=O)(=O)NCCOP(=O)(O)O)c3cccc1c23`
CHEMBL1096338	P9WHE9	—	434.4 Da LogP 2.62 TPSA 132.8	✓ Ro5	✓ Clean	`O=C1Nc2ccc(S(=O)(=O)NCCCCC(F)(F)P(=O)(O)O)c3ccc…`
CHEMBL1097476	P9WHE9	—	386.3 Da LogP 1.18 TPSA 142.0	✓ Ro5	✓ Clean	`O=C1Nc2ccc(S(=O)(=O)NCCCOP(=O)(O)O)c3cccc1c23`
CHEMBL1097477	P9WHE9	—	400.3 Da LogP 1.57 TPSA 142.0	✓ Ro5	✓ Clean	`O=C1Nc2ccc(S(=O)(=O)NCCCCOP(=O)(O)O)c3cccc1c23`
CHEMBL1097478	P9WHE9	—	414.4 Da LogP 1.96 TPSA 142.0	✓ Ro5	✓ Clean	`O=C1Nc2ccc(S(=O)(=O)NCCCCCOP(=O)(O)O)c3cccc1c23`

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
ZINC4096380	1.000	326.3 Da LogP -2.88 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1nc2c(=O)[nH]c(=O)nc-2n(C[C@H](O)[C@H](O)[C@H…`
ZINC11691612	0.714	320.4 Da LogP 1.72 TPSA 84.5	✓ Ro5	✓ Clean	`COCCCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC2896979	0.691	306.3 Da LogP 1.07 TPSA 95.5	✓ Ro5	✓ Clean	`O=C1Nc2ccc(S(=O)(=O)NCCCO)c3cccc1c23`
ZINC1773977	0.690	362.4 Da LogP 2.33 TPSA 112.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC1926250	0.679	306.3 Da LogP 1.33 TPSA 84.5	✓ Ro5	✓ Clean	`COCCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC3869414	0.667	276.2 Da LogP -3.87 TPSA 184.7	1 viol.	✓ Clean	`Nc1c(NC[C@H](O)[C@H](O)[C@H](O)CO)[nH]c(=O)[nH]…`
ZINC5555398	0.661	304.4 Da LogP 2.48 TPSA 75.3	✓ Ro5	✓ Clean	`CCCCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC4129042	0.655	334.4 Da LogP 1.55 TPSA 112.6	✓ Ro5	✓ Clean	`O=C(O)CCCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC2184748	0.655	290.3 Da LogP 2.09 TPSA 75.3	✓ Ro5	✓ Clean	`CCCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC2494770	0.655	292.3 Da LogP 0.68 TPSA 95.5	✓ Ro5	✓ Clean	`O=C1Nc2ccc(S(=O)(=O)NCCO)c3cccc1c23`
ZINC11565587	0.647	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](O)…`
ZINC1532585	0.647	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC1769096	0.647	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC2036848	0.647	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC3650334	0.647	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC3831422	0.647	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](O)…`
ZINC3831423	0.647	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC3831424	0.647	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC4430517	0.635	404.4 Da LogP -1.22 TPSA 161.6	✓ Ro5	✓ Clean	`CCc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)…`
ZINC4129043	0.627	333.4 Da LogP 1.64 TPSA 78.5	✓ Ro5	✓ Clean	`CN(C)CCCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC4353346	0.623	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1ccc2c(nc3c(=O)[nH]c(=O)nc-3n2C[C@H](O)[C@H](…`
ZINC2055807	0.621	352.4 Da LogP 2.93 TPSA 75.3	✓ Ro5	✓ Clean	`O=C1Nc2ccc(S(=O)(=O)NCCc3ccccc3)c3cccc1c23`
ZINC8715467	0.621	320.3 Da LogP 1.16 TPSA 112.6	✓ Ro5	✓ Clean	`O=C(O)CCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC4353342	0.615	406.4 Da LogP -2.36 TPSA 181.8	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC4353343	0.615	406.4 Da LogP -2.36 TPSA 181.8	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](O)…`
ZINC4353344	0.615	406.4 Da LogP -2.36 TPSA 181.8	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC4353345	0.615	406.4 Da LogP -2.36 TPSA 181.8	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC2004116	0.611	396.8 Da LogP -1.38 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2c(cc1Cl)nc1c(=O)[nH]c(=O)nc-1n2C[C@H](O)[…`
ZINC8715483	0.607	361.5 Da LogP 2.42 TPSA 78.5	✓ Ro5	✓ Clean	`CCN(CC)CCCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC3650235	0.600	377.4 Da LogP -2.45 TPSA 187.6	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC4430211	0.600	396.8 Da LogP -1.38 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC5545623	0.600	377.4 Da LogP -2.45 TPSA 187.6	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](O)…`
ZINC5545624	0.600	377.4 Da LogP -2.45 TPSA 187.6	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC5545628	0.600	377.4 Da LogP -2.45 TPSA 187.6	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC828931	0.593	319.4 Da LogP 1.25 TPSA 78.5	✓ Ro5	✓ Clean	`CN(C)CCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC4129045	0.590	386.9 Da LogP 3.58 TPSA 75.3	✓ Ro5	✓ Clean	`O=C1Nc2ccc(S(=O)(=O)NCCc3ccc(Cl)cc3)c3cccc1c23`
ZINC209888	0.589	276.3 Da LogP 1.70 TPSA 75.3	✓ Ro5	✓ Clean	`CCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC43763773	0.589	410.8 Da LogP -1.12 TPSA 161.6	✓ Ro5	✓ Clean	`CCc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)…`
ZINC43763774	0.589	410.8 Da LogP -1.12 TPSA 161.6	✓ Ro5	✓ Clean	`CCc1cc2c(cc1Cl)nc1c(=O)[nH]c(=O)nc-1n2C[C@H](O)…`
ZINC32916615	0.587	382.4 Da LogP 2.94 TPSA 84.5	✓ Ro5	✓ Clean	`COc1ccccc1CCNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC828930	0.586	306.3 Da LogP 0.77 TPSA 112.6	✓ Ro5	✓ Clean	`O=C(O)CNS(=O)(=O)c1ccc2c3c(cccc13)C(=O)N2`
ZINC4430765	0.585	447.2 Da LogP -1.67 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO)c3…`
ZINC4430766	0.585	447.2 Da LogP -1.67 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO)c…`
ZINC4430767	0.585	447.2 Da LogP -1.67 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)c…`
ZINC4430768	0.585	447.2 Da LogP -1.67 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)…`
ZINC1574811	0.579	378.3 Da LogP -2.33 TPSA 170.8	✓ Ro5	✓ Clean	`COc1ccc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](…`
ZINC1657214	0.579	203.6 Da LogP -0.33 TPSA 94.8	✓ Ro5	✓ Clean	`CC(=O)Nc1c(Cl)[nH]c(=O)[nH]c1=O`
ZINC35653106	0.579	405.4 Da LogP -1.97 TPSA 164.8	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC5386869	0.579	378.3 Da LogP -2.33 TPSA 170.8	✓ Ro5	✓ Clean	`COc1ccc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O…`
ZINC5386872	0.579	378.3 Da LogP -2.33 TPSA 170.8	✓ Ro5	✓ Clean	`COc1ccc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H]…`

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.