Protein profile

KP13_05136

Riboflavin synthase alpha chain

Genome: KpKP13

Gene: ribE AHE44255.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYZ0

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Amino acids 211

Annotations 4

Features 26

PDB binders 3

Druggability 0.27

Overview

Basic information about this protein and its source genome.

Accession: KP13_05136
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ribE AHE44255.1
Status: annotated
Amino acids: 211
Structure source: AlphaFold + ColabFold

2.5.1.9

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0004746 Catalysis of the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine + H+ = 5-amino-6-(D-ribitylamino)uracil + riboflavin. 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
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 89.756
DEG E-value: 8.08e-137
Localization: Cytoplasmic
ColabFold pLDDT: 96.92

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 0.27

Structure A0A0H3GYZ0

Pocket Pocket 6

P2Rank 0.051

Structure A0A0H3GYZ0

Pocket Pocket 1

ColabFold model

FPocket 0.415 · Pocket 9

P2Rank 0.04 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 144 / 4744 genomes with a hit

Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

2.5.1.9

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0004746 Catalysis of the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine + H+ = 5-amino-6-(D-ribitylamino)uracil + riboflavin.
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.

26 records

Show feature table

Start	End	DB	Term	Name
1	89	FunFam	G3DSA:2.40.30.20:FF:000003	Riboflavin synthase, alpha subunit
1	93	SUPERFAMILY	SSF63380	Riboflavin synthase domain-like
1	93	InterPro	IPR017938	Riboflavin synthase-like beta-barrel
3	87	Pfam	PF00677	Lumazine binding domain
3	87	InterPro	IPR026017	Lumazine-binding domain
100	185	Pfam	PF00677	Lumazine binding domain
100	185	InterPro	IPR026017	Lumazine-binding domain
98	195	ProSiteProfiles	PS51177	Riboflavin synthase alpha chain lumazine-binding repeat profile.
98	195	InterPro	IPR026017	Lumazine-binding domain
1	89	Gene3D	G3DSA:2.40.30.20	-
1	89	InterPro	IPR023366	ATP synthase subunit alpha, N-terminal domain-like superfamily
102	206	FunFam	G3DSA:2.40.30.20:FF:000005	Riboflavin synthase, alpha subunit
1	185	CDD	cd00402	Riboflavin_synthase_like
1	185	InterPro	IPR001783	Lumazine-binding protein
102	207	Gene3D	G3DSA:2.40.30.20	-
102	207	InterPro	IPR023366	ATP synthase subunit alpha, N-terminal domain-like superfamily
94	200	SUPERFAMILY	SSF63380	Riboflavin synthase domain-like
94	200	InterPro	IPR017938	Riboflavin synthase-like beta-barrel
1	97	ProSiteProfiles	PS51177	Riboflavin synthase alpha chain lumazine-binding repeat profile.
1	97	InterPro	IPR026017	Lumazine-binding domain
1	205	PANTHER	PTHR21098	RIBOFLAVIN SYNTHASE ALPHA CHAIN
1	205	InterPro	IPR001783	Lumazine-binding protein
1	203	NCBIfam	TIGR00187	riboflavin synthase
1	203	InterPro	IPR001783	Lumazine-binding protein
1	211	PIRSF	PIRSF000498	Riboflavin_syn_A
1	211	InterPro	IPR001783	Lumazine-binding protein

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_A0A0H3GYZ0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05136	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
6				0.27

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				1.61	0.026
2				1.22	0.011

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
9				0.415

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.

53 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
CRM	1KZL	Q9Y7P0	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	3A3G	C4TPG1	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@…`
RBF	3A35	C4TPG1	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@…`

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
ZINC11565587	1.000	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	1.000	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	1.000	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	1.000	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	1.000	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	1.000	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	1.000	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	1.000	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…`
ZINC4353342	0.957	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	0.957	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	0.957	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	0.957	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	0.860	396.8 Da LogP -1.38 TPSA 161.6	✓ Ro5	✓ Clean	`Cc1cc2c(cc1Cl)nc1c(=O)[nH]c(=O)nc-1n2C[C@H](O)[…`
ZINC149168378	0.857	374.4 Da LogP -0.31 TPSA 141.3	✓ Ro5	✓ Clean	`CC[C@@H](O)[C@@H](O)[C@@H](O)Cn1c2nc(=O)[nH]c(=…`
ZINC3650235	0.843	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	0.843	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	0.843	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	0.843	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	0.843	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…`
ZINC4430517	0.820	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)…`
ZINC35653106	0.811	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)[…`
ZINC4430765	0.765	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	0.765	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	0.765	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	0.765	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)…`
ZINC43763773	0.759	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	0.759	410.8 Da LogP -1.12 TPSA 161.6	✓ Ro5	✓ Clean	`CCc1cc2c(cc1Cl)nc1c(=O)[nH]c(=O)nc-1n2C[C@H](O)…`
ZINC13513101	0.750	456.4 Da LogP -1.90 TPSA 204.9	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC3831425	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC3831426	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](O)…`
ZINC3831427	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC3831428	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC8551105	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H](O…`
ZINC8551106	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](O)…`
ZINC8551108	0.750	456.3 Da LogP -1.61 TPSA 208.1	1 viol.	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[…`
ZINC4430761	0.717	412.8 Da LogP -2.33 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO)c3…`
ZINC4430762	0.717	412.8 Da LogP -2.33 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO)c…`
ZINC4430763	0.717	412.8 Da LogP -2.33 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)c…`
ZINC4430764	0.717	412.8 Da LogP -2.33 TPSA 181.8	1 viol.	✓ Clean	`O=c1nc2n(C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO)…`
ZINC1574811	0.714	378.3 Da LogP -2.33 TPSA 170.8	✓ Ro5	✓ Clean	`COc1ccc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@H](…`
ZINC5386869	0.714	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…`
ZINC5386870	0.714	378.3 Da LogP -2.33 TPSA 170.8	✓ Ro5	✓ Clean	`COc1ccc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@@H](…`
ZINC5386872	0.714	378.3 Da LogP -2.33 TPSA 170.8	✓ Ro5	✓ Clean	`COc1ccc2nc3c(=O)[nH]c(=O)nc-3n(C[C@@H](O)[C@@H]…`
ZINC1666569	0.680	286.3 Da LogP 0.19 TPSA 100.9	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(CCO)c2cc1C`
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](…`
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…`

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.