Protein profile

KP13_02298

Threonine-phosphate decarboxylase

Genome: KpKP13

Gene: AHE42869.1 cobD Structure source: AlphaFold + ColabFold UniProt A0A0H3GSL5
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Amino acids 358
Annotations 6
Features 14
PDB binders 5
Druggability 0.535

Overview

Basic information about this protein and its source genome.

Accession
KP13_02298
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42869.1 cobD
Status
annotated
Amino acids
358
Structure source
AlphaFold + ColabFold
EC
4.1.1.81
GO
GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. 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:0009236 The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. GO:0048472 Catalysis of the reaction: O-phospho-L-threonine + H+ = (R)-1-aminopropan-2-yl phosphate + CO2.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.1

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 0.535
Structure A0A0H3GSL5
Pocket Pocket 1
P2Rank 0.833
Structure A0A0H3GSL5
Pocket Pocket 1
ColabFold model
FPocket 0.526 · Pocket 3
P2Rank 0.875 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 46 / 4744 genomes with a hit
Normalized 0.01

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • 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:0009236 The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
  • GO:0048472 Catalysis of the reaction: O-phospho-L-threonine + H+ = (R)-1-aminopropan-2-yl phosphate + CO2.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
27 355 CDD cd00609 AAT_like
26 354 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
26 354 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
5 357 SUPERFAMILY SSF53383 PLP-dependent transferases
5 357 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
26 353 Pfam PF00155 Aminotransferase class I and II
26 353 InterPro IPR004839 Aminotransferase, class I/classII
213 226 ProSitePatterns PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site.
213 226 InterPro IPR004838 Aminotransferases, class-I, pyridoxal-phosphate-binding site
38 262 Gene3D G3DSA:3.40.640.10 -
38 262 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
8 354 NCBIfam TIGR01140 threonine-phosphate decarboxylase CobD
8 354 InterPro IPR005860 L-threonine-O-3-phosphate decarboxylase
16 355 PANTHER PTHR42885 HISTIDINOL-PHOSPHATE AMINOTRANSFERASE-RELATED

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_A0A0H3GSL5
AlphaFold — — full sequence — Viewing
ColabFold KP13_02298
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 0.535
16 0.012
7 0.003
10 0.003

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 22.84 0.833
2 7.21 0.315
3 2.67 0.064
4 1.95 0.034
5 1.3 0.012

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.

34 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
144
3CQ5
Q9KJU4 122.1 Da LogP -1.72 TPSA 60.7 ✓ Ro5 ✓ Clean C[N+](CO)(CO)CO
33P
1LC8
P97084 386.2 Da LogP 0.29 TPSA 178.7 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC[C@@H](C)OP(=O)(O)O…
HSA
1FG3
P06986 221.2 Da LogP -0.61 TPSA 121.5 ✓ Ro5 ✓ Clean c1c(nc[nH]1)CC(COP(=O)(O)O)N
PMP
1FG7
P06986 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
TPO
1LC7
P97084 199.1 Da LogP -1.10 TPSA 130.1 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C(=O)O)N)OP(=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.