Protein target profile

HT085_RS00350

bifunctional riboflavin kinase/FAD synthetase

Genome: NZ_AP023069.1 Gene: ribF TUM19854C_00580 3D evidence: ColabFold model

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Length 306

Direct ligand evidence 0 53 total records

Functional annotation 0 EC 0 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: Hit
Gut microbiome off-target: Hit

Essentiality

Essential (DEG): Y

Localization

Localization: Cytoplasmic

Binding-site evidence

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket Medium

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MKIRPGRHNAPDFPHGAAVTIGNFDGVHLGHKHILQKLRLEADTRGLPVVAVVFEPQPKEFFALRTGKTPPCRISPLRTKLELLEGTGCVDAAWVLRFDRNFSEISAQAFIDRLLRQTLNTRYLLVGDDFRFGAGREGCFELLAQQPDMQTERTPSVIVEDIRTSSTAVRQALSDGNLAYAKKLLGHDYVLGGRVVHGRKLGRTLNAPTANIRLPGHRYALGGVFVVEADGAFGTRRGVASFGFNPTVDGGCSQKLEVHLFDFQGDLYGQRLNVRFLHKLRDEEKFDGMEELKRRIEADMEAAKCW

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

No GO or EC annotations are currently loaded for this protein.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
7	304	PANTHER	PTHR22749	RIBOFLAVIN KINASE/FMN ADENYLYLTRANSFERASE
7	304	InterPro	IPR023468	Riboflavin kinase
17	176	SUPERFAMILY	SSF52374	Nucleotidylyl transferase
289	306	Coils	Coil	Coil
175	305	SUPERFAMILY	SSF82114	Riboflavin kinase-like
175	305	InterPro	IPR023465	Riboflavin kinase domain superfamily
189	306	Gene3D	G3DSA:2.40.30.30	-
189	306	InterPro	IPR023465	Riboflavin kinase domain superfamily
184	305	SMART	SM00904	Flavokinase_2
184	305	InterPro	IPR015865	Riboflavin kinase domain, bacterial/eukaryotic
1	187	Gene3D	G3DSA:3.40.50.620	HUPs
1	187	InterPro	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold
19	306	NCBIfam	TIGR00083	riboflavin biosynthesis protein RibF
19	306	InterPro	IPR002606	Riboflavin kinase, bacterial
17	198	CDD	cd02064	FAD_synthetase_N
17	198	InterPro	IPR015864	FAD synthetase
1	186	FunFam	G3DSA:3.40.50.620:FF:000021	Riboflavin biosynthesis protein
3	306	PIRSF	PIRSF004491	RibF_RibC
3	306	InterPro	IPR002606	Riboflavin kinase, bacterial
185	304	Pfam	PF01687	Riboflavin kinase
185	304	InterPro	IPR015865	Riboflavin kinase domain, bacterial/eukaryotic
13	168	Pfam	PF06574	FAD synthetase
13	168	InterPro	IPR015864	FAD synthetase

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1

0.673

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Surrounding area

Site 2 FPocket #3

0.254

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Surrounding area

All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
ColabFold HT085_RS00350	ColabFold	—	—	full sequence	—	Viewing

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

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

LUM PDB via homolog 242.2 Da · LogP 0.78 · TPSA 91.5 Open detail RCSB PDB

PPV PDB via homolog Detail RCSB PDB

RBF PDB via homolog Detail RCSB PDB

ZINC11565587 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC12446789 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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
LUM RCSB PDB	1S4M	Q9WZW1	242.2 Da LogP 0.78 TPSA 91.5	✓ Ro5	✓ Clean	`Cc1cc2c(cc1C)nc3c(n2)C(=O)NC(=O)N3`
PPV RCSB PDB	2X0K	Q59263	178.0 Da LogP -0.81 TPSA 124.3	✓ Ro5	✓ Clean	`OP(=O)(O)OP(=O)(O)O`
RBF RCSB PDB	1NB9	Q969G6	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 ZINC	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)…`
ZINC12446789 ZINC	1.000	242.2 Da LogP 0.78 TPSA 91.5	✓ Ro5	✓ Clean	`Cc1cc2nc3[nH]c(=O)[nH]c(=O)c3nc2cc1C`
ZINC1532585 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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)…`
ZINC113969374 ZINC	0.714	228.2 Da LogP 0.47 TPSA 91.5	✓ Ro5	✓ Clean	`Cc1ccc2nc3c(=O)[nH]c(=O)[nH]c3nc2c1`
ZINC1574811 ZINC	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 ZINC	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 ZINC	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 ZINC	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]…`
ZINC6827739 ZINC	0.692	258.0 Da LogP -0.69 TPSA 170.8	✓ Ro5	✓ Clean	`O=P(O)(O)OP(=O)(O)OP(=O)(O)O`
ZINC1666569 ZINC	0.680	286.3 Da LogP 0.19 TPSA 100.9	✓ Ro5	✓ Clean	`Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(CCO)c2cc1C`
ZINC1703511 ZINC	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 ZINC	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 ZINC	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)…`

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.