Protein profile

KP13_01793

Lysine decarboxylase, constitutive

Genome: KpKP13

Gene: ldcC AHE46233.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GMX3
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Amino acids 729
Annotations 10
Features 28
PDB binders 1
Druggability 0.248

Overview

Basic information about this protein and its source genome.

Accession
KP13_01793
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
ldcC AHE46233.1
Status
annotated
Amino acids
729
Structure source
AlphaFold + ColabFold
EC
4.1.1.18
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups. GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound. 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008792 Catalysis of the reaction: L-arginine + H+ = agmatine + 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
92.63

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 0.248
Structure A0A0H3GMX3
Pocket Pocket 3
P2Rank 0.865
Structure A0A0H3GMX3
Pocket Pocket 1
ColabFold model
FPocket 0.894 · Pocket 23
P2Rank 0.815 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 99 / 4744 genomes with a hit
Normalized 0.021

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008792 Catalysis of the reaction: L-arginine + H+ = agmatine + CO2.
  • GO:0008923 Catalysis of the reaction: L-lysine + H+ = cadaverine + CO2.
  • 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:0006527 The chemical reactions and pathways resulting in the breakdown of L-arginine.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
143 453 CDD cd00615 Orn_deC_like
143 453 InterPro IPR000310 Orn/Lys/Arg decarboxylase, major domain
7 724 PIRSF PIRSF009393 Orn_decarb
7 724 InterPro IPR011193 Ornithine/lysine/arginine decarboxylase
142 436 Gene3D G3DSA:3.40.640.10 -
142 436 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
142 556 Pfam PF01276 Orn/Lys/Arg decarboxylase, major domain
142 556 InterPro IPR000310 Orn/Lys/Arg decarboxylase, major domain
13 141 Gene3D G3DSA:3.40.50.2300 -
142 436 FunFam G3DSA:3.40.640.10:FF:000008 Lysine decarboxylase, inducible
27 136 Pfam PF03709 Orn/Lys/Arg decarboxylase, N-terminal domain
27 136 InterPro IPR005308 Orn/Lys/Arg decarboxylase, N-terminal
31 719 PANTHER PTHR45229 CONSTITUTIVE ORNITHINE DECARBOXYLASE
31 719 InterPro IPR011193 Ornithine/lysine/arginine decarboxylase
579 720 SUPERFAMILY SSF55904 Ornithine decarboxylase C-terminal domain
579 720 InterPro IPR036633 Orn/Lys/Arg decarboxylase, C-terminal domain superfamily
374 388 ProSitePatterns PS00703 Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site.
374 388 InterPro IPR000310 Orn/Lys/Arg decarboxylase, major domain
142 574 SUPERFAMILY SSF53383 PLP-dependent transferases
142 574 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
607 724 FunFam G3DSA:3.90.100.10:FF:000001 Lysine decarboxylase, inducible
603 723 Gene3D G3DSA:3.90.100.10 -
437 602 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
437 602 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
437 457 Coils Coil Coil
582 712 Pfam PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain
582 712 InterPro IPR008286 Orn/Lys/Arg decarboxylase, C-terminal
437 602 FunFam G3DSA:3.90.1150.10:FF:000016 Lysine decarboxylase, inducible

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_A0A0H3GMX3
AlphaFold — — full sequence — Viewing
ColabFold KP13_01793
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
3 0.248
7 0.236

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 14.73 0.733
2 7.67 0.406
3 3.76 0.144
4 2.98 0.097
5 2.35 0.061

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.

51 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
G4P
3N75
P0A9H3 603.2 Da LogP -2.22 TPSA 345.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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.