Protein profile

KP13_01807

1-deoxy-D-xylulose 5-phosphate reductoisomerase

Genome: KpKP13

Gene: dxr AHE46247.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GJN7
Amino acids 400
Annotations 8
Features 24
PDB binders 7
Druggability 0.956

Overview

Basic information about this protein and its source genome.

Accession
KP13_01807
Gene
dxr AHE46247.1
Status
annotated
Amino acids
400
Structure source
AlphaFold + ColabFold

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 (%)
80.402
DEG E-value
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
97.11

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 0.956
Structure A0A0H3GJN7
Pocket Pocket 1
P2Rank 0.943
Structure A0A0H3GJN7
Pocket Pocket 1
ColabFold model
FPocket 0.905 · Pocket 1
P2Rank 0.948 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 205 / 4744 genomes with a hit
Normalized 0.043

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:0070402 Binding to the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
  • GO:0046872 Binding to a metal ion.
  • GO:0030604 Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + NADP+ = 1-deoxy-D-xylulose 5-phosphate + H+ + NADPH.
  • GO:0005515 Binding to a protein.
  • 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:0030145 Binding to a manganese ion (Mn).
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
2 150 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
2 150 InterPro IPR036291 NAD(P)-binding domain superfamily
301 395 SUPERFAMILY SSF69055 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
301 395 InterPro IPR036169 DXP reductoisomerase, C-terminal domain superfamily
4 392 Hamap MF_00183 1-deoxy-D-xylulose 5-phosphate reductoisomerase [dxr].
4 392 InterPro IPR003821 1-deoxy-D-xylulose 5-phosphate reductoisomerase
1 15 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
271 387 Pfam PF13288 DXP reductoisomerase C-terminal domain
271 387 InterPro IPR026877 DXP reductoisomerase C-terminal domain
1 150 Gene3D G3DSA:3.40.50.720 -
1 399 PIRSF PIRSF006205 Dxp_reductoisomrs
1 399 InterPro IPR003821 1-deoxy-D-xylulose 5-phosphate reductoisomerase
312 398 Gene3D G3DSA:1.10.1740.10 -
4 132 Pfam PF02670 1-deoxy-D-xylulose 5-phosphate reductoisomerase
4 132 InterPro IPR013512 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal
1 150 FunFam G3DSA:3.40.50.720:FF:000045 1-deoxy-D-xylulose 5-phosphate reductoisomerase
126 274 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
1 397 NCBIfam TIGR00243 1-deoxy-D-xylulose-5-phosphate reductoisomerase
1 397 InterPro IPR003821 1-deoxy-D-xylulose 5-phosphate reductoisomerase
146 239 Pfam PF08436 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain
146 239 InterPro IPR013644 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal
2 393 PANTHER PTHR30525 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
2 393 InterPro IPR003821 1-deoxy-D-xylulose 5-phosphate reductoisomerase
312 397 FunFam G3DSA:1.10.1740.10:FF:000004 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.

3D visualization script Full viewer

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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_A0A0H3GJN7
AlphaFold full sequence Viewing
ColabFold KP13_01807
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 0.956
4 0.488
22 0.341

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 19.95 0.847
2 3.47 0.126
3 1.37 0.016

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.