Protein profile

PA3975

phosphomethylpyrimidine kinase

Genome: NC_002516.2

Gene: PA3975 thiD Structure source: AlphaFold UniProt Q9HX41
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Amino acids 265
Annotations 6
Features 10
PDB binders 5
Druggability 0.559

Overview

Basic information about this protein and its source genome.

Accession
PA3975
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3975 thiD
Status
annotated
Amino acids
265
Structure source
AlphaFold
EC
2.7.1.49
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:0008902 Catalysis of the reaction: 4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-methyl-5-phosphomethylpyrimidine + ADP + 2 H+. GO:0008972 Catalysis of the reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine. 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: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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Periplasmic

Selected Druggability evidence

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 0.559
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008902 Catalysis of the reaction: 4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-methyl-5-phosphomethylpyrimidine + ADP + 2 H+.
  • GO:0008972 Catalysis of the reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine.
  • 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: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.

10 records
Show feature table
Start End DB Term Name
17 253 Pfam PF08543 Phosphomethylpyrimidine kinase
17 253 InterPro IPR013749 Pyridoxamine kinase/Phosphomethylpyrimidine kinase
7 255 PANTHER PTHR20858 PHOSPHOMETHYLPYRIMIDINE KINASE
9 246 CDD cd01169 HMPP_kinase
9 246 InterPro IPR004399 Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain
1 259 FunFam G3DSA:3.40.1190.20:FF:000060 Phosphomethylpyrimidine kinase
6 255 SUPERFAMILY SSF53613 Ribokinase-like
6 255 InterPro IPR029056 Ribokinase-like
1 259 Gene3D G3DSA:3.40.1190.20 -
1 259 InterPro IPR029056 Ribokinase-like

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA3975
AlphaFold — — full sequence — Viewing
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
2 0.559
1 0.259

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.

55 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
ACP
4C5M
A0A0H3JTP0 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
HMH
1JXI
P55882 139.2 Da LogP -0.14 TPSA 72.0 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CO
PE4
5ZW9
A0A0F7J8S0 354.4 Da LogP 0.11 TPSA 84.8 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCO
PXL
4C5L
A0A0H3JTP0 167.2 Da LogP 0.40 TPSA 70.4 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)CO)C=O)O
UEG
4C5L
A0A0H3JTP0 169.2 Da LogP 0.08 TPSA 73.6 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)CO)CO)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.