Protein profile

KP13_31610

Phosphomethylpyrimidine synthase

Genome: KpKP13

Gene: thiC AHE46927.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GKP1

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Amino acids 631

Annotations 9

Features 17

PDB binders 3

Druggability 0.903

Overview

Basic information about this protein and its source genome.

Accession: KP13_31610
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: thiC AHE46927.1
Status: annotated
Amino acids: 631
Structure source: AlphaFold + ColabFold

4.1.99.17

GO:0009228 The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver. GO:0016830 Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0070284 Catalysis of the reaction: 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + CO + 5'-deoxyadenosine + formate + L-methionine + 3 H+.

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 (%): 71.944
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 92.62

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 0.903

Structure A0A0H3GKP1

Pocket Pocket 1

P2Rank 0.852

Structure A0A0H3GKP1

Pocket Pocket 1

ColabFold model

FPocket 0.92 · Pocket 1

P2Rank 0.923 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 739 / 4744 genomes with a hit

Normalized 0.156

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

4.1.99.17

Gene Ontology (GO)

GO:0009228 The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
GO:0016830 Catalysis of the cleavage of C-C bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0070284 Catalysis of the reaction: 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + CO + 5'-deoxyadenosine + formate + L-methionine + 3 H+.
GO:0008270 Binding to a zinc ion (Zn).
GO:0009229 The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
148	596	SFLD	SFLDF00407	phosphomethylpyrimidine synthase (ThiC)
148	596	InterPro	IPR002817	Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B
218	531	FunFam	G3DSA:3.20.20.540:FF:000001	Phosphomethylpyrimidine synthase
218	531	Gene3D	G3DSA:3.20.20.540	Radical SAM ThiC family, central domain
218	531	InterPro	IPR038521	ThiC/Bza, core domain
532	566	Gene3D	G3DSA:6.10.250.620	-
6	620	PANTHER	PTHR30557	THIAMINE BIOSYNTHESIS PROTEIN THIC
6	620	InterPro	IPR002817	Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B
148	596	Pfam	PF01964	Radical SAM ThiC family
8	628	SFLD	SFLDS00113	Radical SAM Phosphomethylpyrimidine Synthase
147	600	Hamap	MF_00089	Phosphomethylpyrimidine synthase [thiC].
147	600	InterPro	IPR037509	Phosphomethylpyrimidine synthase
23	625	SFLD	SFLDG01114	phosphomethylpyrimidine synthase (ThiC)
27	107	Pfam	PF13667	ThiC-associated domain
27	107	InterPro	IPR025747	ThiC-associated domain
147	599	NCBIfam	TIGR00190	phosphomethylpyrimidine synthase
147	599	InterPro	IPR002817	Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B

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_A0A0H3GKP1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_31610	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				0.903

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	15.61	0.757
2	12.4	0.649
3	3.55	0.131
4	3.12	0.105
5	1.53	0.023

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				0.92

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	12.67	0.658
3	7.12	0.37
4	3.69	0.14
5	2.05	0.045

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
5AD	4S27	O82392	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O`
AIR	4S27	O82392	295.2 Da LogP -1.81 TPSA 160.3	✓ Ro5	✓ Clean	`c1c(n(cn1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(…`
IRN	4S25	O82392	280.2 Da LogP -1.39 TPSA 134.3	✓ Ro5	✓ Clean	`c1cn(cn1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=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
ZINC100352250	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O`
ZINC1095430	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]1O`
ZINC13542750	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H]…`
ZINC135734	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]1O`
ZINC17005625	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]1O`
ZINC1999286	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O`
ZINC3869309	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]1O`
ZINC3869310	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]…`
ZINC3869311	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H]…`
ZINC3869312	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC1702626	0.974	281.3 Da LogP -1.59 TPSA 139.5	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H]…`
ZINC4821676	0.974	281.3 Da LogP -1.59 TPSA 139.5	✓ Ro5	✓ Clean	`C[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC4821679	0.974	281.3 Da LogP -1.59 TPSA 139.5	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H]…`
ZINC4821682	0.974	281.3 Da LogP -1.59 TPSA 139.5	✓ Ro5	✓ Clean	`C[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC5139067	0.721	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC2047403	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1O`
ZINC2047673	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC2169830	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC3201876	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC3201878	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC3814316	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC3830178	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3830179	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3978047	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC3978048	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC3978049	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC4048240	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC4773848	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC4773849	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H…`
ZINC4773850	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC4773851	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@…`
ZINC77981211	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]…`
ZINC82228511	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]1O`
ZINC8580514	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC895113	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC896706	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC970363	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC1081541	0.689	285.7 Da LogP -0.73 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CCl)[C@@H](O)[C@@H]…`
ZINC4188096	0.689	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188103	0.689	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC4188112	0.689	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188116	0.689	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC5941240	0.689	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CF)[C@@H](O)[C@H]1O`
ZINC100349915	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H…`
ZINC12501834	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@…`
ZINC1318753	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]…`
ZINC25963247	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]…`
ZINC3869319	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H…`
ZINC5929300	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]…`
ZINC895091	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[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.