Protein profile

PA4044

1-deoxy-D-xylulose-5-phosphate synthase

Genome: NC_002516.2

Gene: PA4044 dxs Structure source: AlphaFold UniProt Q9KGU7
Amino acids 627
Annotations 9
Features 31
PDB binders 10
Druggability 0.615

Overview

Basic information about this protein and its source genome.

Accession
PA4044
Gene
PA4044 dxs
Status
annotated
Amino acids
627
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
25.043
Human E-value
3.599999999999999e-24
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

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 0.615
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MPKTLHEIPRERPATPLLDRASSPAELRRLGEADLETLADELRQYLLYTVGQTGGHFGAGLGVVELTIALHYVFDTPDDRLVWDVGHQAYPHKILTERRELMGTLRQKNGLAAFPRRAESEYDTFGVGHSSTSISAALGMAIAARLQGKERKSVAVIGDGALTAGMAFEALNHASEVDADMLVILNDNDMSISHNVGGLSNYLAKILSSRTYSSMREGSKKVLSRLPGAWEIARRTEEYAKGMLVPGTLFEELGWNYIGPIDGHDLPTLVATLRNMRDMKGPQFLHVVTKKGKGFAPAELDPIGYHAITKLEAPGSAPKKTGGPKYSSVFGQWLCDMAAQDARLLGITPAMKEGSDLVAFSERYPERYFDVAIAEQHAVTLAAGMACEGMKPVVAIYSTFLQRAYDQLIHDVAVQHLDVLFAIDRAGLVGEDGPTHAGSFDISYLRCIPGMLVMTPSDEDELRKLLTTGYLFDGPAAVRYPRGSGPNHPIDPDLQPVEIGKGVVRRRGGRVALLVFGVQLAEAMKVAESLDATVVDMRFVKPLDEALVRELAGSHELLVTIEENAVMGGAGSAVGEFLASEGLEVPLLQLGLPDYYVEHAKPSEMLAECGLDAAGIEKAVRQRLDRQ

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008661 Catalysis of the reaction: D-glyceraldehyde 3-phosphate + H+ + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
  • GO:0019288 The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
  • GO:0016114 The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.
  • 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:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
15 386 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
15 386 InterPro IPR029061 Thiamin diphosphate-binding fold
22 624 NCBIfam TIGR00204 1-deoxy-D-xylulose-5-phosphate synthase
22 624 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
18 289 Pfam PF13292 1-deoxy-D-xylulose-5-phosphate synthase
18 289 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
500 616 Pfam PF02780 Transketolase, C-terminal domain
500 616 InterPro IPR033248 Transketolase, C-terminal domain
500 625 FunFam G3DSA:3.40.50.920:FF:000002 1-deoxy-D-xylulose-5-phosphate synthase
54 295 CDD cd02007 TPP_DXS
54 295 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
323 490 FunFam G3DSA:3.40.50.970:FF:000005 1-deoxy-D-xylulose-5-phosphate synthase
329 482 CDD cd07033 TPP_PYR_DXS_TK_like
323 491 Gene3D G3DSA:3.40.50.970 -
496 625 SUPERFAMILY SSF52922 TK C-terminal domain-like
496 625 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
17 625 Hamap MF_00315 1-deoxy-D-xylulose-5-phosphate synthase [dxs].
17 625 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
430 446 ProSitePatterns PS00802 Transketolase signature 2.
430 446 InterPro IPR020826 Transketolase binding site
321 508 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
321 508 InterPro IPR029061 Thiamin diphosphate-binding fold
500 625 Gene3D G3DSA:3.40.50.920 -
500 625 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
11 298 Gene3D G3DSA:3.40.50.970 -
9 626 PANTHER PTHR43322 1-D-DEOXYXYLULOSE 5-PHOSPHATE SYNTHASE-RELATED
9 626 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
324 488 SMART SM00861 Transket_pyr_3
324 488 InterPro IPR005475 Transketolase-like, pyrimidine-binding domain
325 485 Pfam PF02779 Transketolase, pyrimidine binding domain
325 485 InterPro IPR005475 Transketolase-like, pyrimidine-binding domain

3D Structure

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

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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 PA4044
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
1 0.615

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.

90 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
1U0 P29401 483.4 Da LogP 1.12 TPSA 205.5 1 viol. ✓ Clean Cc1c(sc(c1Cc2cnc(nc2N)C)[C@@H](CO)O)CCOP(=O)(O)…
1Y7 P29401 292.2 Da LogP -4.11 TPSA 188.1 1 viol. ✓ Clean C([C@@H]([C@H]([C@@H]([C@@H]([C@@H](COP(=O)(O)O…
COI P09061 130.1 Da LogP 0.69 TPSA 54.4 ✓ Ro5 ✓ Clean CC(C)CC(=O)C(=O)O
DPO P77488 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([O-])[O-]
DX5 P29401 232.1 Da LogP -2.83 TPSA 147.7 1 viol. ✓ Clean C([C@@H]([C@H]([C@@H](COP(=O)(O)O)O)O)O)O
HTL Q9RUB5 467.4 Da LogP 1.04 TPSA 186.0 ✓ Ro5 ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)C)CCO[P@@](=O)(…
PYR P21874 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
S6P P29401 262.2 Da LogP -3.47 TPSA 167.9 1 viol. ✓ Clean C([C@@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)…
T6F P29401 685.5 Da LogP -2.79 TPSA 336.9 3 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](CO)([C@H]([C@@H…
TDK Q9RUB5 563.4 Da LogP 0.84 TPSA 235.7 3 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)[P@@](=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.