Protein profile

PA4519

ornithine decarboxylase

Genome: NC_002516.2

Gene: PA4519 speC Structure source: AlphaFold UniProt Q9HVQ3
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Amino acids 387
Annotations 6
Features 39
PDB binders 9
Druggability 0.607

Overview

Basic information about this protein and its source genome.

Accession
PA4519
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA4519 speC
Status
annotated
Amino acids
387
Structure source
AlphaFold
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:0004586 Catalysis of the reaction: L-ornithine + H+ = CO2 + putrescine. GO:0033387 The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from arginine, via decarboxylation of ornithine. 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:0006596 The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
31.304
Human E-value
1.37e-11
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.607
Structure –
Pocket –

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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0004586 Catalysis of the reaction: L-ornithine + H+ = CO2 + putrescine.
  • GO:0033387 The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from arginine, via decarboxylation of ornithine.
  • 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:0006596 The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.

Sequence Features

Domain/signature hits from InterPro and related databases.

39 records
Show feature table
Start End DB Term Name
21 380 Gene3D G3DSA:2.40.37.10 Lyase, Ornithine Decarboxylase; Chain A, domain 1
21 380 InterPro IPR009006 Alanine racemase/group IV decarboxylase, C-terminal
25 273 SUPERFAMILY SSF51419 PLP-binding barrel
25 273 InterPro IPR029066 PLP-binding barrel
52 79 PRINTS PR01182 Ornithine decarboxylase signature
52 79 InterPro IPR002433 Ornithine decarboxylase
96 120 PRINTS PR01182 Ornithine decarboxylase signature
96 120 InterPro IPR002433 Ornithine decarboxylase
126 148 PRINTS PR01182 Ornithine decarboxylase signature
126 148 InterPro IPR002433 Ornithine decarboxylase
26 50 PRINTS PR01182 Ornithine decarboxylase signature
26 50 InterPro IPR002433 Ornithine decarboxylase
329 339 PRINTS PR01182 Ornithine decarboxylase signature
329 339 InterPro IPR002433 Ornithine decarboxylase
35 271 Pfam PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain
35 271 InterPro IPR022644 Orn/DAP/Arg decarboxylase 2, N-terminal
33 273 Gene3D G3DSA:3.20.20.10 Alanine racemase
33 273 InterPro IPR029066 PLP-binding barrel
216 229 ProSitePatterns PS00879 Orn/DAP/Arg decarboxylases family 2 signature 2.
216 229 InterPro IPR022657 Orn/DAP/Arg decarboxylase 2, conserved site
34 269 FunFam G3DSA:3.20.20.10:FF:000008 Ornithine decarboxylase
265 380 FunFam G3DSA:2.40.37.10:FF:000004 Ornithine decarboxylase
23 386 PANTHER PTHR11482 ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE
23 386 InterPro IPR002433 Ornithine decarboxylase
25 387 CDD cd00622 PLPDE_III_ODC
54 72 ProSitePatterns PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.
54 72 InterPro IPR022653 Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site
177 190 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
177 190 InterPro IPR000183 Ornithine/DAP/Arg decarboxylase
74 86 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
74 86 InterPro IPR000183 Ornithine/DAP/Arg decarboxylase
54 72 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
54 72 InterPro IPR000183 Ornithine/DAP/Arg decarboxylase
261 280 PRINTS PR01179 Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
261 280 InterPro IPR000183 Ornithine/DAP/Arg decarboxylase
272 365 Pfam PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet domain
272 365 InterPro IPR022643 Orn/DAP/Arg decarboxylase 2, C-terminal
245 386 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like
245 386 InterPro IPR009006 Alanine racemase/group IV decarboxylase, C-terminal

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA4519
AlphaFold — — full sequence — Viewing
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 0.607

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.

62 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
DMO
2TOD
P07805 182.2 Da LogP -0.23 TPSA 89.3 ✓ Ro5 ✓ Clean C(CC(C(F)F)(C(=O)O)N)CN
GET
1NJJ
Q9TZZ6 496.6 Da LogP -5.61 TPSA 248.4 2 viol. ✓ Clean C[C@H]([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@…
N2P
5GJP
O50657 102.2 Da LogP 0.07 TPSA 52.0 ✓ Ro5 ✓ Clean C(CCN)CCN
ORX
1SZR
P07805 363.3 Da LogP -0.01 TPSA 175.2 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CCCN)C(=O)O)O
PL2
2NVA
Q84527 361.3 Da LogP 0.06 TPSA 173.8 1 viol. ✓ Clean [H]/N=C(/N)\NCCCCNCc1c(cnc(c1O)C)COP(=O)(O)O
PLG
1SZR
P07805 306.2 Da LogP -0.12 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O
PUT
1F3T
P07805 88.2 Da LogP -0.32 TPSA 52.0 ✓ Ro5 ✓ Clean C(CCN)CN
PXP
1SZR
P07805 249.2 Da LogP 0.20 TPSA 120.1 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CO)O
XAP
2ON3
P11926 90.1 Da LogP -0.77 TPSA 61.3 ✓ Ro5 ✓ Clean C(CN)CON

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.