Protein profile

VK055_2182

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

Genome: KpATCC43816

Gene: AIK80787.1 dxs Structure source: Experimental + ColabFold UniProt A6T5F3
Amino acids 620
Annotations 3
Features 33
PDB binders 13
Druggability 0.978

Overview

Basic information about this protein and its source genome.

Accession
VK055_2182
Gene
AIK80787.1 dxs
Status
annotated
Amino acids
620
Structure source
Experimental + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
23.993
Human E-value
8.39e-17
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
91.129
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
91.34

Selected Druggability evidence

PDB experimental structure

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 0.978
Structure 8BZX
Pocket Pocket 1
P2Rank 0.941
Structure 8BZX
Pocket Pocket 1
ColabFold model
FPocket 0.981 · Pocket 1
P2Rank 0.985 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 266 / 4744 genomes with a hit
Normalized 0.056

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • 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.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
47 288 CDD cd02007 TPP_DXS
47 288 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
320 479 Pfam PF02779 Transketolase, pyrimidine binding domain
320 479 InterPro IPR005475 Transketolase-like, pyrimidine-binding domain
317 504 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
317 504 InterPro IPR029061 Thiamin diphosphate-binding fold
13 282 Pfam PF13292 1-deoxy-D-xylulose-5-phosphate synthase
13 282 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
318 486 FunFam G3DSA:3.40.50.970:FF:000005 1-deoxy-D-xylulose-5-phosphate synthase
10 620 Hamap MF_00315 1-deoxy-D-xylulose-5-phosphate synthase [dxs].
10 620 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
319 484 SMART SM00861 Transket_pyr_3
319 484 InterPro IPR005475 Transketolase-like, pyrimidine-binding domain
11 619 NCBIfam TIGR00204 1-deoxy-D-xylulose-5-phosphate synthase
11 619 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
323 478 CDD cd07033 TPP_PYR_DXS_TK_like
425 441 ProSitePatterns PS00802 Transketolase signature 2.
425 441 InterPro IPR020826 Transketolase binding site
492 619 SUPERFAMILY SSF52922 TK C-terminal domain-like
492 619 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
1 291 Gene3D G3DSA:3.40.50.970 -
495 611 Pfam PF02780 Transketolase, C-terminal domain
495 611 InterPro IPR033248 Transketolase, C-terminal domain
318 493 Gene3D G3DSA:3.40.50.970 -
36 55 ProSitePatterns PS00801 Transketolase signature 1.
36 55 InterPro IPR005474 Transketolase, N-terminal
5 619 PANTHER PTHR43322 1-D-DEOXYXYLULOSE 5-PHOSPHATE SYNTHASE-RELATED
5 619 InterPro IPR005477 Deoxyxylulose-5-phosphate synthase
10 381 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
10 381 InterPro IPR029061 Thiamin diphosphate-binding fold
495 620 Gene3D G3DSA:3.40.50.920 -
495 620 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
495 620 FunFam G3DSA:3.40.50.920:FF:000002 1-deoxy-D-xylulose-5-phosphate synthase

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

1 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 8BZX
X-ray 20.00 Å - Viewing
ColabFold VK055_2182
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
2 0.978
1 0.95

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 38.84 0.961
2 32.24 0.942
3 3.54 0.13
4 3.06 0.102
5 1.93 0.04

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.

93 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)…
THV P21953 496.4 Da LogP 1.75 TPSA 189.2 ✓ Ro5 ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](C(C)C)O)CCO[P@@…
THW P21953 530.4 Da LogP 2.14 TPSA 189.2 1 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](c3ccccc3)O)CCO[…
THY P21953 510.4 Da LogP 2.14 TPSA 189.2 1 viol. ✓ Clean CC[C@H](C)[C-](c1[n+](c(c(s1)CCO[P@](=O)(O)OP(=…

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.