Protein profile

HT085_RS00175

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

Genome: NZ_AP023069.1

Gene: TUM19854C_00310 E8M63_03350 dxs Structure source: AlphaFold UniProt A0AAX2TRM6
Amino acids 637
Annotations 8
Features 34
PDB binders 10

Overview

Basic information about this protein and its source genome.

Accession
HT085_RS00175
Gene
TUM19854C_00310 E8M63_03350 dxs
Status
annotated
Amino acids
637
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
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 Medium
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0008661 Catalysis of the reaction: D-glyceraldehyde 3-phosphate + H+ + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO2.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • 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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
329 489 Pfam PF02779 Transketolase, pyrimidine binding domain
329 489 InterPro IPR005475 Transketolase-like, pyrimidine-binding domain
43 294 CDD cd02007 TPP_DXS
43 294 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
225 245 Coils Coil Coil
329 515 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
329 515 InterPro IPR029061 Thiamin diphosphate-binding fold
7 288 Pfam PF13292 1-deoxy-D-xylulose-5-phosphate synthase
7 288 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
334 488 CDD cd07033 TPP_PYR_DXS_TK_like
9 630 NCBIfam TIGR00204 1-deoxy-D-xylulose-5-phosphate synthase
9 630 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
506 631 FunFam G3DSA:3.40.50.920:FF:000002 1-deoxy-D-xylulose-5-phosphate synthase
4 392 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
4 392 InterPro IPR029061 Thiamin diphosphate-binding fold
506 631 Gene3D G3DSA:3.40.50.920 -
506 631 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
1 297 Gene3D G3DSA:3.40.50.970 -
6 631 Hamap MF_00315 1-deoxy-D-xylulose-5-phosphate synthase [dxs].
6 631 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
32 51 ProSitePatterns PS00801 Transketolase signature 1.
32 51 InterPro IPR005474 Transketolase, N-terminal
436 452 ProSitePatterns PS00802 Transketolase signature 2.
436 452 InterPro IPR020826 Transketolase binding site
502 630 SUPERFAMILY SSF52922 TK C-terminal domain-like
502 630 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
330 494 SMART SM00861 Transket_pyr_3
330 494 InterPro IPR005475 Transketolase-like, pyrimidine-binding domain
329 498 Gene3D G3DSA:3.40.50.970 -
3 633 PANTHER PTHR43322 1-D-DEOXYXYLULOSE 5-PHOSPHATE SYNTHASE-RELATED
3 633 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
329 496 FunFam G3DSA:3.40.50.970:FF:000005 1-deoxy-D-xylulose-5-phosphate synthase
506 622 Pfam PF02780 Transketolase, C-terminal domain
506 622 InterPro IPR033248 Transketolase, C-terminal domain

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 HT085_RS00175
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 0.581
2 0.449
3 0.211

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 57.78 0.978
2 3.76 0.117
3 1.82 0.029
4 1.5 0.018

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.