Protein profile

KP13_02801

3,4-dihydroxy-2-butanone 4-phosphate synthase

Genome: KpKP13

Gene: AHE42630.1 ribB Structure source: AlphaFold + ColabFold UniProt A0A0H3H374

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Amino acids 217

Annotations 2

Features 11

PDB binders 3

Druggability 0.056

Overview

Basic information about this protein and its source genome.

Accession: KP13_02801
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42630.1 ribB
Status: annotated
Amino acids: 217
Structure source: AlphaFold + ColabFold

GO:0008686 Catalysis of the reaction: D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H+. 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 (%): 94.47
DEG E-value: 5.21e-151
Localization: Cytoplasmic
ColabFold pLDDT: 95.79

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 0.056

Structure A0A0H3H374

Pocket Pocket 7

P2Rank 0.531

Structure A0A0H3H374

Pocket Pocket 1

ColabFold model

FPocket 0.418 · Pocket 4

P2Rank 0.559 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 597 / 4744 genomes with a hit

Normalized 0.126

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0008686 Catalysis of the reaction: D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H+.
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.

11 records

Show feature table

Start	End	DB	Term	Name
1	217	Gene3D	G3DSA:3.90.870.10	DHBP synthase
7	213	SUPERFAMILY	SSF55821	YrdC/RibB
7	213	InterPro	IPR017945	DHBP synthase RibB-like alpha/beta domain superfamily
3	216	FunFam	G3DSA:3.90.870.10:FF:000002	3,4-dihydroxy-2-butanone 4-phosphate synthase
17	208	Pfam	PF00926	3,4-dihydroxy-2-butanone 4-phosphate synthase
17	208	InterPro	IPR000422	3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB
13	209	NCBIfam	TIGR00506	3,4-dihydroxy-2-butanone-4-phosphate synthase
13	209	InterPro	IPR000422	3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB
11	213	Hamap	MF_00180	3,4-dihydroxy-2-butanone 4-phosphate synthase [ribB].
11	213	InterPro	IPR000422	3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB
12	210	PANTHER	PTHR21327	GTP CYCLOHYDROLASE II-RELATED

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_A0A0H3H374	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02801	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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				8.25	0.44
2				1.68	0.029

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				0.418

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				7.97	0.424
2				1.52	0.022

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
5RP	1TKU	Q5A3V6	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`C([C@H]([C@H](C(=O)CO)O)O)OP(=O)(O)O`
5SP	3LQU	P66032	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`C([C@H]([C@@H](C(=O)CO)O)O)OP(=O)(O)O`
RES	4P6C	Q9KKP2	231.1 Da LogP -2.68 TPSA 156.5	1 viol.	✓ Clean	`C([C@H]([C@H](C(=O)NO)O)O)OP(=O)(O)O`

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
ZINC1529626	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC30320708	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC100065511	0.793	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC100085043	0.793	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC104869937	0.793	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC13537943	0.793	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC85994845	0.793	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC5132038	0.767	290.2 Da LogP -3.90 TPSA 185.0	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC3870277	0.724	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC5830339	0.594	231.1 Da LogP -2.68 TPSA 156.5	1 viol.	✓ Clean	`O=C(NO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC5975509	0.586	202.1 Da LogP -2.19 TPSA 127.5	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)CO`
ZINC12502210	0.576	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC12502212	0.576	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC12502214	0.576	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC12502216	0.576	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC4523251	0.576	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@@H](O)COP(…`
ZINC4523255	0.576	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@H](O)COP(=…`
ZINC4523257	0.576	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@@H](O)COP(=…`
ZINC4523259	0.576	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)COP(=O…`
ZINC31259596	0.563	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)CO`
ZINC31259600	0.563	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)CO`
ZINC3869804	0.563	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)CO`
ZINC3869805	0.563	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)CO`
ZINC2516111	0.548	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC2522704	0.548	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC3869812	0.548	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC12501558	0.545	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(…`
ZINC12501560	0.545	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O…`
ZINC12501562	0.545	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)…`
ZINC12501564	0.545	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(…`
ZINC1532623	0.545	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(…`
ZINC2047359	0.545	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC2545091	0.545	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O…`
ZINC3869602	0.545	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC3869603	0.545	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC3869604	0.545	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC1560408815	0.514	339.1 Da LogP -1.87 TPSA 214.1	1 viol.	✓ Clean	`[O]/C(COP(=O)(O)O)=C(/O)[C@H](O)[C@H](O)COP(=O)…`
ZINC100033330	0.500	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC100067275	0.500	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC12503760	0.500	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532601	0.500	200.1 Da LogP -1.98 TPSA 124.3	✓ Ro5	✓ Clean	`O=C[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC19850142	0.500	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC2508229	0.500	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4545927	0.500	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=O)(…`
ZINC4887586	0.500	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887587	0.500	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887588	0.500	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887589	0.500	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)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.