Protein profile

KP13_01975

Riboflavin biosynthesis protein ribF

Genome: KpKP13

Gene: ribF AHE46414.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GJ01

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Amino acids 295

Annotations 6

Features 23

PDB binders 3

Druggability 0.387

Overview

Basic information about this protein and its source genome.

Accession: KP13_01975
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ribF AHE46414.1
Status: annotated
Amino acids: 295
Structure source: AlphaFold + ColabFold

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:0003919 Catalysis of the reaction: ATP + FMN = diphosphate + FAD. GO:0008531 Catalysis of the reaction: ATP + riboflavin = ADP + FMN + 2 H+. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0006747 The chemical reactions and pathways resulting in the formation of FAD, the oxidized form of flavin-adenine dinucleotide. GO:0009398 The chemical reactions and pathways resulting in the formation of FMN, the oxidized form of flavin mononucleotide (riboflavin 5'-(dihydrogen phosphate)), which acts as a coenzyme for a number of oxidative enzymes including NADH dehydrogenase.

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 (%): 90.476
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 92.96

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 0.387

Structure A0A0H3GJ01

Pocket Pocket 4

P2Rank 0.937

Structure A0A0H3GJ01

Pocket Pocket 1

ColabFold model

FPocket 0.497 · Pocket 3

P2Rank 0.867 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 159 / 4744 genomes with a hit

Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

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:0003919 Catalysis of the reaction: ATP + FMN = diphosphate + FAD.
GO:0008531 Catalysis of the reaction: ATP + riboflavin = ADP + FMN + 2 H+.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0006747 The chemical reactions and pathways resulting in the formation of FAD, the oxidized form of flavin-adenine dinucleotide.
GO:0009398 The chemical reactions and pathways resulting in the formation of FMN, the oxidized form of flavin mononucleotide (riboflavin 5'-(dihydrogen phosphate)), which acts as a coenzyme for a number of oxidative enzymes including NADH dehydrogenase.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
2	150	Pfam	PF06574	FAD synthetase
2	150	InterPro	IPR015864	FAD synthetase
169	293	FunFam	G3DSA:2.40.30.30:FF:000001	Riboflavin biosynthesis protein
167	288	Pfam	PF01687	Riboflavin kinase
167	288	InterPro	IPR015865	Riboflavin kinase domain, bacterial/eukaryotic
157	290	SUPERFAMILY	SSF82114	Riboflavin kinase-like
157	290	InterPro	IPR023465	Riboflavin kinase domain superfamily
2	180	CDD	cd02064	FAD_synthetase_N
2	180	InterPro	IPR015864	FAD synthetase
2	158	SUPERFAMILY	SSF52374	Nucleotidylyl transferase
166	290	SMART	SM00904	Flavokinase_2
166	290	InterPro	IPR015865	Riboflavin kinase domain, bacterial/eukaryotic
1	295	PIRSF	PIRSF004491	RibF_RibC
1	295	InterPro	IPR002606	Riboflavin kinase, bacterial
1	168	FunFam	G3DSA:3.40.50.620:FF:000021	Riboflavin biosynthesis protein
3	287	PANTHER	PTHR22749	RIBOFLAVIN KINASE/FMN ADENYLYLTRANSFERASE
3	287	InterPro	IPR023468	Riboflavin kinase
1	168	Gene3D	G3DSA:3.40.50.620	HUPs
1	168	InterPro	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold
169	294	Gene3D	G3DSA:2.40.30.30	-
169	294	InterPro	IPR023465	Riboflavin kinase domain superfamily
2	289	NCBIfam	TIGR00083	riboflavin biosynthesis protein RibF
2	289	InterPro	IPR002606	Riboflavin kinase, bacterial

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_A0A0H3GJ01	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01975	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
4				0.387
18				0.273

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	Score	Probability
1	14.56	0.726
2	11.7	0.621
3	8.76	0.469

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
3				0.497
4				0.303

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	Score	Probability
1	14.35	0.72
2	12.45	0.651
3	11.57	0.616

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
LUM	1S4M	Q9WZW1	242.2 Da LogP 0.78 TPSA 91.5	✓ Ro5	✓ Clean	`Cc1cc2c(cc1C)nc3c(n2)C(=O)NC(=O)N3`
PPV	2X0K	Q59263	178.0 Da LogP -0.81 TPSA 124.3	✓ Ro5	✓ Clean	`OP(=O)(O)OP(=O)(O)O`
RBF	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	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	1.000	242.2 Da LogP 0.78 TPSA 91.5	✓ Ro5	✓ Clean	`Cc1cc2nc3[nH]c(=O)[nH]c(=O)c3nc2cc1C`
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)…`
ZINC113969374	0.714	228.2 Da LogP 0.47 TPSA 91.5	✓ Ro5	✓ Clean	`Cc1ccc2nc3c(=O)[nH]c(=O)[nH]c3nc2c1`
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]…`
ZINC6827739	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	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)…`

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.