Protein profile

KP13_02748

Ornithine decarboxylase, constitutive

Genome: KpKP13

Gene: AHE42684.1 speC Structure source: AlphaFold + ColabFold UniProt A0A0H3GYC4
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Amino acids 712
Annotations 9
Features 31
PDB binders 1
Druggability 0.724

Overview

Basic information about this protein and its source genome.

Accession
KP13_02748
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42684.1 speC
Status
annotated
Amino acids
712
Structure source
AlphaFold + ColabFold
EC
4.1.1.17
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:0004586 Catalysis of the reaction: L-ornithine + H+ = CO2 + putrescine.

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
95.46

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 0.724
Structure A0A0H3GYC4
Pocket Pocket 1
P2Rank 0.874
Structure A0A0H3GYC4
Pocket Pocket 1
ColabFold model
FPocket 0.854 · Pocket 30
P2Rank 0.87 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 261 / 4744 genomes with a hit
Normalized 0.055

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • 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:0004586 Catalysis of the reaction: L-ornithine + H+ = CO2 + putrescine.
  • 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:0008295 The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
413 592 FunFam G3DSA:3.90.1150.10:FF:000032 Ornithine decarboxylase SpeF
101 412 Gene3D G3DSA:3.40.640.10 -
101 412 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
568 697 Pfam PF03711 Orn/Lys/Arg decarboxylase, C-terminal domain
568 697 InterPro IPR008286 Orn/Lys/Arg decarboxylase, C-terminal
342 356 ProSitePatterns PS00703 Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site.
342 356 InterPro IPR000310 Orn/Lys/Arg decarboxylase, major domain
1 100 SUPERFAMILY SSF52172 CheY-like
1 100 InterPro IPR011006 CheY-like superfamily
1 100 Gene3D G3DSA:3.40.50.220 -
1 100 InterPro IPR027464 Ornithine decarboxylase, N-terminal
413 592 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
413 592 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
101 412 FunFam G3DSA:3.40.640.10:FF:000008 Lysine decarboxylase, inducible
4 79 Pfam PF03709 Orn/Lys/Arg decarboxylase, N-terminal domain
4 79 InterPro IPR005308 Orn/Lys/Arg decarboxylase, N-terminal
101 558 SUPERFAMILY SSF53383 PLP-dependent transferases
101 558 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
2 712 PIRSF PIRSF009393 Orn_decarb
2 712 InterPro IPR011193 Ornithine/lysine/arginine decarboxylase
593 712 Gene3D G3DSA:3.90.100.10 -
563 711 SUPERFAMILY SSF55904 Ornithine decarboxylase C-terminal domain
563 711 InterPro IPR036633 Orn/Lys/Arg decarboxylase, C-terminal domain superfamily
102 428 CDD cd00615 Orn_deC_like
102 428 InterPro IPR000310 Orn/Lys/Arg decarboxylase, major domain
593 712 FunFam G3DSA:3.90.100.10:FF:000001 Lysine decarboxylase, inducible
9 711 PANTHER PTHR45229 CONSTITUTIVE ORNITHINE DECARBOXYLASE
9 711 InterPro IPR011193 Ornithine/lysine/arginine decarboxylase
101 543 Pfam PF01276 Orn/Lys/Arg decarboxylase, major domain
101 543 InterPro IPR000310 Orn/Lys/Arg decarboxylase, major domain
1 100 FunFam G3DSA:3.40.50.220:FF:000002 Ornithine decarboxylase, constitutive

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_A0A0H3GYC4
AlphaFold — — full sequence — Viewing
ColabFold KP13_02748
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 0.724
23 0.407

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 16.81 0.788
2 5.1 0.234
3 2.89 0.092
4 2.59 0.074
5 2.54 0.072

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.