Protein profile

KP13_31513

Indole-3-pyruvate decarboxylase

Genome: KpKP13

Gene: AHE43376.1 ipdC Structure source: AlphaFold + ColabFold UniProt A0A0H3GRC2
Amino acids 555
Annotations 7
Features 25
PDB binders 15
Druggability 0.615

Overview

Basic information about this protein and its source genome.

Accession
KP13_31513
Gene
AHE43376.1 ipdC
Status
annotated
Amino acids
555
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 (%)
43.433
DEG E-value
1.82e-171
Localization
CytoplasmicMembrane
ColabFold pLDDT
95.7

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 0.615
Structure A0A0H3GRC2
Pocket Pocket 5
P2Rank 0.403
Structure A0A0H3GRC2
Pocket Pocket 1
ColabFold model
FPocket 0.861 · Pocket 1
P2Rank 0.495 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 66 / 4744 genomes with a hit
Normalized 0.014

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
  • 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: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:0000287 Binding to a magnesium (Mg) ion.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004737 Catalysis of the reaction: a 2-oxo acid = an aldehyde + CO2.
  • GO:0000949 The chemical reactions and pathways involving the catabolism of aromatic amino acids to produce aromatic alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When an aromatic family amino acid, phenylalanine, tyrosine, or tryptophan, is used as the substrate, 2-phenylethanol, 4-hydroxyphenylethanol, or tryptophol, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
353 545 FunFam G3DSA:3.40.50.970:FF:000024 Pyruvate decarboxylase isozyme
8 177 Pfam PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
8 177 InterPro IPR012001 Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain
5 188 FunFam G3DSA:3.40.50.970:FF:000019 Pyruvate decarboxylase isozyme
359 546 Gene3D G3DSA:3.40.50.970 -
7 178 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
7 178 InterPro IPR029061 Thiamin diphosphate-binding fold
11 170 CDD cd07038 TPP_PYR_PDC_IPDC_like
11 170 InterPro IPR047213 Pyruvate decarboxylase/indolepyruvate decarboxylase-like, pyrimidine-binding domain
362 542 CDD cd02005 TPP_PDC_IPDC
362 542 InterPro IPR047214 Pyruvate decarboxylase/indolepyruvate decarboxylase-like, PP-binding domain
190 349 Gene3D G3DSA:3.40.50.1220 -
360 546 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
360 546 InterPro IPR029061 Thiamin diphosphate-binding fold
202 319 Pfam PF00205 Thiamine pyrophosphate enzyme, central domain
202 319 InterPro IPR012000 Thiamine pyrophosphate enzyme, central domain
396 530 Pfam PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
396 530 InterPro IPR011766 Thiamine pyrophosphate enzyme, TPP-binding
4 544 PANTHER PTHR43452 PYRUVATE DECARBOXYLASE
4 544 InterPro IPR012110 Pyruvate decarboxylase/indolepyruvate decarboxylase-like
169 339 SUPERFAMILY SSF52467 DHS-like NAD/FAD-binding domain
169 339 InterPro IPR029035 DHS-like NAD/FAD-binding domain superfamily
4 186 Gene3D G3DSA:3.40.50.970 -
2 554 PIRSF PIRSF036565 Pyruvt_ip_decrb
2 554 InterPro IPR012110 Pyruvate decarboxylase/indolepyruvate decarboxylase-like

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_A0A0H3GRC2
AlphaFold full sequence Viewing
ColabFold KP13_31513
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
6 0.131
16 0.006
1 0.002
2 0.001

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 8.8 0.403
2 5.23 0.2
3 4.66 0.167
4 2.18 0.043
5 1.47 0.017

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.

68 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
2OP P06169 90.1 Da LogP -0.55 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@@H](C(=O)O)O
ALK Q12629 140.1 Da LogP 0.16 TPSA 66.8 ✓ Ro5 ✓ Clean C[C@H](O)P(=O)(O)OC
ALU Q12629 138.1 Da LogP 0.36 TPSA 63.6 ✓ Ro5 ✓ Clean CC(=O)[P@](=O)(O)OC
DPX P06672 430.3 Da LogP 0.21 TPSA 197.3 1 viol. ✓ Clean Cc1ncc(c(n1)N)CN/C(=C(/[C@@H](CO[P@](=O)(O)OP(=…
KPV P51852 192.2 Da LogP 1.66 TPSA 54.4 ✓ Ro5 ✓ Clean c1ccc(cc1)CCCC(=O)C(=O)O
PPY P51852 164.2 Da LogP 0.88 TPSA 54.4 ✓ Ro5 ✓ Clean c1ccc(cc1)CC(=O)C(=O)O
PY0 P06169 106.1 Da LogP -2.67 TPSA 89.5 ✓ Ro5 ✓ Clean C[C@@H]([C@@](N)(O)[O-])O
PYM P06169 87.1 Da LogP -0.94 TPSA 60.2 ✓ Ro5 ✓ Clean CC(=O)C(=O)N
PYR P06169 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
R1T P51852 467.4 Da LogP 2.15 TPSA 185.3 ✓ Ro5 ✓ Clean Cc1c(sc(c1Cc2cnc(nc2N)C)[C@@H](C)O)CCO[P@](=O)(…
S1T P51852 467.4 Da LogP 2.15 TPSA 185.3 ✓ Ro5 ✓ Clean Cc1c(sc(c1Cc2cnc(nc2N)C)[C@H](C)O)CCO[P@](=O)(O…
TDL P06672 513.4 Da LogP 0.13 TPSA 226.5 2 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](C)(C(=O)O)O)CCO…
TLA P51852 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O
TPU P06672 408.2 Da LogP 0.08 TPSA 195.8 ✓ Ro5 ✓ Clean Cc1c(nnn1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
TPW P51852 423.3 Da LogP 2.10 TPSA 165.1 ✓ Ro5 ✓ Clean Cc1c(csc1CCO[P@@](=O)(O)OP(=O)(O)O)Cc2cnc(nc2N)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.