Protein profile

KP13_02045

6,7-dimethyl-8-ribityllumazine synthase

Genome: KpKP13

Gene: ribH AHE46048.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GJ29

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Amino acids 156

Annotations 5

Features 15

PDB binders 8

Druggability 0.681

Overview

Basic information about this protein and its source genome.

Accession: KP13_02045
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ribH AHE46048.1
Status: annotated
Amino acids: 156
Structure source: AlphaFold + ColabFold

2.5.1.78

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). 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:0009349 An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 (%): 100.0
DEG E-value: 9.180000000000001e-110
Localization: Cytoplasmic
ColabFold pLDDT: 98.07

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 0.681

Structure A0A0H3GJ29

Pocket Pocket 1

P2Rank 0.204

Structure A0A0H3GJ29

Pocket Pocket 1

ColabFold model

FPocket 0.513 · Pocket 1

P2Rank 0.259 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 1145 / 4744 genomes with a hit

Normalized 0.241

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)

2.5.1.78

Gene Ontology (GO)

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).
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:0009349 An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
15	148	CDD	cd09209	Lumazine_synthase-I
15	148	InterPro	IPR034964	Lumazine synthase
14	150	NCBIfam	TIGR00114	6,7-dimethyl-8-ribityllumazine synthase
14	150	InterPro	IPR034964	Lumazine synthase
1	156	FunFam	G3DSA:3.40.50.960:FF:000001	6,7-dimethyl-8-ribityllumazine synthase
4	154	SUPERFAMILY	SSF52121	Lumazine synthase
4	154	InterPro	IPR036467	Lumazine/riboflavin synthase superfamily
9	155	PANTHER	PTHR21058	6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE DMRL SYNTHASE LUMAZINE SYNTHASE
9	155	InterPro	IPR034964	Lumazine synthase
1	156	Gene3D	G3DSA:3.40.50.960	Lumazine/riboflavin synthase
1	156	InterPro	IPR036467	Lumazine/riboflavin synthase superfamily
8	154	Hamap	MF_00178	6,7-dimethyl-8-ribityllumazine synthase [ribH].
8	154	InterPro	IPR034964	Lumazine synthase
13	151	Pfam	PF00885	6,7-dimethyl-8-ribityllumazine synthase
13	151	InterPro	IPR002180	Lumazine/riboflavin 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 + 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_A0A0H3GJ29	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02045	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				0.681

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				3.64	0.137

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				0.513

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				3.67	0.139

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.

58 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)…`
CRM	1KYX	Q9UUB1	386.3 Da LogP -4.13 TPSA 218.8	1 viol.	✓ Clean	`C(CC(=O)O)C1=NC2=C(NC(=O)NC2=O)N(C1=O)C[C@@H]([…`
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(=…`
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(=…`
RBF	1KYV	Q9UUB1	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@…`
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]([…`

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
ZINC1703511	0.679	375.4 Da LogP -1.12 TPSA 148.7	✓ Ro5	✓ Clean	`Cc1cc2cc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](O)…`
ZINC4878448	0.679	375.4 Da LogP -1.12 TPSA 148.7	✓ Ro5	✓ Clean	`Cc1cc2cc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC4878449	0.679	375.4 Da LogP -1.12 TPSA 148.7	✓ Ro5	✓ Clean	`Cc1cc2cc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC4878453	0.679	375.4 Da LogP -1.12 TPSA 148.7	✓ Ro5	✓ Clean	`Cc1cc2cc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC4353346	0.673	376.4 Da LogP -1.72 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1ccc2c(nc3c(=O)[nH]c(=O)nc-3n2C[C@H](O)[C@H](…`
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]…`
ZINC4096380	0.647	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…`
ZINC1731984	0.643	392.4 Da LogP -2.49 TPSA 175.6	✓ Ro5	✓ Clean	`Cc1cc2c(cc1C)[n+]([O-])c1c(=O)[nH]c(=O)nc-1n2C[…`
ZINC5011745	0.643	392.4 Da LogP -2.49 TPSA 175.6	✓ Ro5	✓ Clean	`Cc1cc2c(cc1C)[n+]([O-])c1c(=O)[nH]c(=O)nc-1n2C[…`
ZINC5011746	0.643	392.4 Da LogP -2.49 TPSA 175.6	✓ Ro5	✓ Clean	`Cc1cc2c(cc1C)[n+]([O-])c1c(=O)[nH]c(=O)nc-1n2C[…`
ZINC5011747	0.643	392.4 Da LogP -2.49 TPSA 175.6	✓ Ro5	✓ Clean	`Cc1cc2c(cc1C)[n+]([O-])c1c(=O)[nH]c(=O)nc-1n2C[…`
ZINC1602641	0.615	284.3 Da LogP 0.40 TPSA 97.7	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(CC=O)c2cc1C`
ZINC43214974	0.607	373.4 Da LogP -0.51 TPSA 124.3	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(CCN(CCO)CCO)c2cc1C`
ZINC1712550	0.596	342.4 Da LogP 1.15 TPSA 106.9	✓ Ro5	✓ Clean	`CCC(=O)OCCn1c2nc(=O)[nH]c(=O)c-2nc2cc(C)c(C)cc21`
ZINC1666568	0.589	328.3 Da LogP 0.76 TPSA 106.9	✓ Ro5	✓ Clean	`CC(=O)OCCn1c2nc(=O)[nH]c(=O)c-2nc2cc(C)c(C)cc21`
ZINC4878473	0.561	347.3 Da LogP -1.74 TPSA 148.7	✓ Ro5	✓ Clean	`O=c1nc2n(C[C@H](O)[C@H](O)[C@H](O)CO)c3ccccc3cc…`
ZINC4878477	0.561	347.3 Da LogP -1.74 TPSA 148.7	✓ Ro5	✓ Clean	`O=c1nc2n(C[C@@H](O)[C@H](O)[C@H](O)CO)c3ccccc3c…`
ZINC4878479	0.561	347.3 Da LogP -1.74 TPSA 148.7	✓ Ro5	✓ Clean	`O=c1nc2n(C[C@H](O)[C@@H](O)[C@H](O)CO)c3ccccc3c…`
ZINC4878481	0.561	347.3 Da LogP -1.74 TPSA 148.7	✓ Ro5	✓ Clean	`O=c1nc2n(C[C@@H](O)[C@@H](O)[C@H](O)CO)c3ccccc3…`
ZINC391159	0.560	256.3 Da LogP 0.74 TPSA 80.6	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C)c2cc1C`
ZINC100069844	0.542	363.3 Da LogP -2.03 TPSA 168.9	1 viol.	✓ Clean	`O=c1nc2n(C[C@H](O)[C@H](O)[C@H](O)CO)c3cc(O)ccc…`
ZINC1666570	0.541	386.4 Da LogP 0.61 TPSA 144.2	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(CCOC(=O)CCC(=O)O)c…`
ZINC43214973	0.541	393.8 Da LogP -0.17 TPSA 124.3	✓ Ro5	✓ Clean	`Cc1cc2c(cc1Cl)nc1c(=O)[nH]c(=O)nc-1n2CCN(CCO)CCO`
ZINC1870669	0.534	353.4 Da LogP -0.09 TPSA 137.1	✓ Ro5	✓ Clean	`COC(=O)Nc1nc2cc(C)c(C)cc2n1C[C@@H](O)[C@@H](O)[…`
ZINC4830947	0.534	353.4 Da LogP -0.09 TPSA 137.1	✓ Ro5	✓ Clean	`COC(=O)Nc1nc2cc(C)c(C)cc2n1C[C@H](O)[C@H](O)[C@…`
ZINC4830948	0.534	353.4 Da LogP -0.09 TPSA 137.1	✓ Ro5	✓ Clean	`COC(=O)Nc1nc2cc(C)c(C)cc2n1C[C@@H](O)[C@H](O)[C…`
ZINC4830949	0.534	353.4 Da LogP -0.09 TPSA 137.1	✓ Ro5	✓ Clean	`COC(=O)Nc1nc2cc(C)c(C)cc2n1C[C@H](O)[C@@H](O)[C…`
ZINC11565587	0.533	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	0.533	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	0.533	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	0.533	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	0.533	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	0.533	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	0.533	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	0.533	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	0.525	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)…`
ZINC4353442	0.524	357.4 Da LogP 0.02 TPSA 131.1	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C/C=N/NC(N)=S)c2cc…`
ZINC8580591	0.524	357.4 Da LogP 0.02 TPSA 131.1	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C/C=N\NC(N)=S)c2cc…`
ZINC1722914	0.516	393.8 Da LogP -0.17 TPSA 124.3	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(CCN(CCO)CCO)c2cc1Cl`
ZINC5012547	0.516	455.4 Da LogP -1.00 TPSA 195.2	1 viol.	✓ Clean	`Cc1cc2cc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC1562485	0.508	374.4 Da LogP -0.51 TPSA 135.8	✓ Ro5	✓ Clean	`Cc1cc2cc3c(=O)[nH]c(=O)cc-3n(C[C@@H](O)[C@H](O)…`
ZINC5372514	0.508	374.4 Da LogP -0.51 TPSA 135.8	✓ Ro5	✓ Clean	`Cc1cc2cc3c(=O)[nH]c(=O)cc-3n(C[C@H](O)[C@H](O)[…`
ZINC5372517	0.508	374.4 Da LogP -0.51 TPSA 135.8	✓ Ro5	✓ Clean	`Cc1cc2cc3c(=O)[nH]c(=O)cc-3n(C[C@H](O)[C@@H](O)…`
ZINC5372519	0.508	374.4 Da LogP -0.51 TPSA 135.8	✓ Ro5	✓ Clean	`Cc1cc2cc3c(=O)[nH]c(=O)cc-3n(C[C@@H](O)[C@@H](O…`
ZINC4353342	0.508	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	0.508	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	0.508	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…`
ZINC4430765	0.508	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	0.508	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	0.508	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)…`

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.