Protein profile

PA3650

1-deoxy-D-xylulose 5-phosphate reductoisomerase

Genome: NC_002516.2

Gene: PA3650 dxr Structure source: AlphaFold UniProt Q9KGU6
Amino acids 396
Annotations 8
Features 23
PDB binders 7
Druggability 0.539

Overview

Basic information about this protein and its source genome.

Accession
PA3650
Gene
PA3650 dxr
Status
annotated
Amino acids
396
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

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

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 0.539
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:0030604 Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + NADP+ = 1-deoxy-D-xylulose 5-phosphate + H+ + NADPH.
  • GO:0030145 Binding to a manganese ion (Mn).
  • GO:0070402 Binding to the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
  • GO:0051484 OBSOLETE. The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway that contributes to terpenoid biosynthesis. 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:0008299 The chemical reactions and pathways resulting in the formation of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
  • GO:0046872 Binding to a metal ion.
  • GO:0005515 Binding to a protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
6 389 NCBIfam TIGR00243 1-deoxy-D-xylulose-5-phosphate reductoisomerase
6 389 InterPro IPR003821 1-deoxy-D-xylulose 5-phosphate reductoisomerase
149 237 Pfam PF08436 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain
149 237 InterPro IPR013644 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal
2 153 FunFam G3DSA:3.40.50.720:FF:000045 1-deoxy-D-xylulose 5-phosphate reductoisomerase
300 393 SUPERFAMILY SSF69055 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
300 393 InterPro IPR036169 DXP reductoisomerase, C-terminal domain superfamily
269 385 Pfam PF13288 DXP reductoisomerase C-terminal domain
269 385 InterPro IPR026877 DXP reductoisomerase C-terminal domain
7 390 Hamap MF_00183 1-deoxy-D-xylulose 5-phosphate reductoisomerase [dxr].
7 390 InterPro IPR003821 1-deoxy-D-xylulose 5-phosphate reductoisomerase
4 153 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
4 153 InterPro IPR036291 NAD(P)-binding domain superfamily
3 390 PANTHER PTHR30525 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
3 390 InterPro IPR003821 1-deoxy-D-xylulose 5-phosphate reductoisomerase
1 153 Gene3D G3DSA:3.40.50.720 -
310 395 FunFam G3DSA:1.10.1740.10:FF:000004 1-deoxy-D-xylulose 5-phosphate reductoisomerase
7 135 Pfam PF02670 1-deoxy-D-xylulose 5-phosphate reductoisomerase
7 135 InterPro IPR013512 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal
129 272 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
311 395 Gene3D G3DSA:1.10.1740.10 -
4 396 PIRSF PIRSF006205 Dxp_reductoisomrs
4 396 InterPro IPR003821 1-deoxy-D-xylulose 5-phosphate reductoisomerase

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 PA3650
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 0.539
10 0.378

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.

99 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
C0K P45568 309.2 Da LogP 1.81 TPSA 98.1 ✓ Ro5 ✓ Clean CN(C(=O)CC[C@@H](c1ccc(c(c1)F)F)P(=O)(O)O)O
CBQ P45568 302.5 Da LogP 0.79 TPSA 140.0 ✓ Ro5 ✓ Clean c1cc(ncc1Cl)NC(P(=O)(O)O)P(=O)(O)O
DXP P45568 214.1 Da LogP -1.59 TPSA 124.3 ✓ Ro5 ✓ Clean CC(=O)[C@H]([C@@H](COP(=O)(O)O)O)O
IMB P45568 318.2 Da LogP 1.29 TPSA 140.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)ccnc2NC(P(=O)(O)O)P(=O)(O)O
SRT Q8DBF5 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@H]([C@H](C(=O)O)O)(C(=O)O)O
SYC P45568 173.1 Da LogP 0.76 TPSA 70.4 ✓ Ro5 ✓ Clean c1ccnc(c1)CP(=O)(O)O
SYE P45568 223.2 Da LogP 1.91 TPSA 70.4 ✓ Ro5 ✓ Clean c1ccc2c(c1)ccc(n2)CP(=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.