Protein profile

VK055_2778

3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase

Genome: KpATCC43816

Gene: iolD AIK81367.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLT3
Amino acids 646
Annotations 5
Features 23
PDB binders 19
Druggability 0.87

Overview

Basic information about this protein and its source genome.

Accession
VK055_2778
Gene
iolD AIK81367.1
Status
annotated
Amino acids
646
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
31.818
Human E-value
1.05e-07
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
26.976
Localization
Cytoplasmic
ColabFold pLDDT
97.3

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 0.87
Structure A0A0H3GLT3
Pocket Pocket 9
P2Rank 0.838
Structure A0A0H3GLT3
Pocket Pocket 1
ColabFold model
FPocket 0.992 · Pocket 1
P2Rank 0.839 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 241 / 4744 genomes with a hit
Normalized 0.051

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0016823 Catalysis of the hydrolysis of any carbon-carbon bond in a ketonic substance, a substance containing a keto (C=O) group.
  • 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:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
  • GO:0019310 The chemical reactions and pathways resulting in the breakdown of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
  • GO:0000287 Binding to a magnesium (Mg) ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
185 367 SUPERFAMILY SSF52467 DHS-like NAD/FAD-binding domain
185 367 InterPro IPR029035 DHS-like NAD/FAD-binding domain superfamily
419 630 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
419 630 InterPro IPR029061 Thiamin diphosphate-binding fold
214 393 Gene3D G3DSA:3.40.50.1220 -
409 641 Gene3D G3DSA:3.40.50.970 -
478 497 ProSitePatterns PS00187 Thiamine pyrophosphate enzymes signature.
478 497 InterPro IPR000399 TPP-binding enzyme, conserved site
3 208 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
3 208 InterPro IPR029061 Thiamin diphosphate-binding fold
442 601 Pfam PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
442 601 InterPro IPR011766 Thiamine pyrophosphate enzyme, TPP-binding
5 644 NCBIfam TIGR04377 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing)
5 644 InterPro IPR030817 3,5/4-Trihydroxycyclohexa-1,2-dione hydrolase
220 353 Pfam PF00205 Thiamine pyrophosphate enzyme, central domain
220 353 InterPro IPR012000 Thiamine pyrophosphate enzyme, central domain
10 188 CDD cd07035 TPP_PYR_POX_like
7 196 Pfam PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
7 196 InterPro IPR012001 Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain
421 624 CDD cd02003 TPP_IolD
5 608 PANTHER PTHR18968 THIAMINE PYROPHOSPHATE ENZYMES
5 608 InterPro IPR045229 Thiamine pyrophosphate enzyme
3 209 Gene3D G3DSA:3.40.50.970 -

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

Loading 3D structure...

Legend High Medium Low

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_A0A0H3GLT3
AlphaFold full sequence Viewing
ColabFold VK055_2778
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
9 0.87
2 0.676

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 25.62 0.908
2 10.41 0.559
3 2.94 0.095
4 1.2 0.01
5 0.49 0.0

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.

77 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
1MM P07342 381.4 Da LogP 0.49 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1nc(nc(n1)OC)NC(=O)NS(=O)(=O)c2ccccc2C(=O)OC
AUJ P07342 Cc1ncc(c(n1)N)C[N]2=C(SC(=C2C)CCOP(=O)(O)OP(=O)…
AYD P07342 382.3 Da LogP 0.98 TPSA 177.1 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN/C(=C/CCO[P@@](=O)(O)OP(=O)(O)O…
CIE P07342 414.8 Da LogP 1.83 TPSA 136.6 ✓ Ro5 ✓ Clean CCOC(=O)c1ccccc1S(=O)(=O)NC(=O)Nc2nc(cc(n2)Cl)OC
CO2 P07342 44.0 Da LogP -0.58 TPSA 34.1 ✓ Ro5 ✓ Clean C(=O)=O
DTT P07342 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
F50 P07342 76.1 Da LogP 0.02 TPSA 46.5 ✓ Ro5 ✓ Clean CC(=O)OO
HTL P07342 467.4 Da LogP 1.04 TPSA 186.0 ✓ Ro5 ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)C)CCO[P@@](=O)(…
NSP P07342 138.2 Da LogP -0.17 TPSA 77.8 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN
OXY P07342 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=O
P22 P07342 206.0 Da LogP 0.23 TPSA 113.3 ✓ Ro5 ✓ Clean CCO[P@](=O)(O)OP(=O)(O)O
P23 P07342 220.1 Da LogP 0.62 TPSA 113.3 ✓ Ro5 ✓ Clean CCCO[P@@](=O)(O)OP(=O)(O)O
P25 P07342 248.1 Da LogP 1.40 TPSA 113.3 ✓ Ro5 ✓ Clean CCCCCO[P@@](=O)(O)OP(=O)(O)O
PXD P07342 483.4 Da LogP 2.61 TPSA 116.9 ✓ Ro5 ✓ Clean COc1cnc(n2c1nc(n2)NS(=O)(=O)c3c(cccc3OCC(F)F)C(…
PYD P07342 123.2 Da LogP 0.68 TPSA 51.8 ✓ Ro5 ✓ Clean Cc1cnc(nc1N)C
PYR P07342 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
TP9 P07342 412.3 Da LogP -0.03 TPSA 182.8 1 viol. ✓ Clean Cc1ncc(c(n1)N)CN/C(=C(/CCO[P@](=O)([O-])O[P@@](…
YF3 P07342 212.3 Da LogP 0.78 TPSA 63.8 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CNC(C)CS
YF4 P07342 180.3 Da LogP 0.82 TPSA 55.0 ✓ Ro5 ✓ Clean CCN(C)Cc1cnc(nc1N)C

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.