Protein profile

PA2876

orotidine 5'-phosphate decarboxylase

Genome: NC_002516.2

Gene: PA2876 pyrF Structure source: AlphaFold UniProt Q59654
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Amino acids 232
Annotations 5
Features 18
PDB binders 5
Druggability 0.758

Overview

Basic information about this protein and its source genome.

Accession
PA2876
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA2876 pyrF
Status
annotated
Amino acids
232
Structure source
AlphaFold
EC
4.1.1.23
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0004590 Catalysis of the reaction: H+ + orotidine 5'-phosphate = CO2 + UMP. GO:0006207 The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors. GO:0044205 The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD+ or oxygen.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
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 0.758
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004590 Catalysis of the reaction: H+ + orotidine 5'-phosphate = CO2 + UMP.
  • GO:0006207 The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
  • GO:0044205 The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD+ or oxygen.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
8 216 CDD cd04725 OMP_decarboxylase_like
1 230 PANTHER PTHR32119 OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
1 230 InterPro IPR014732 Orotidine 5'-phosphate decarboxylase
9 227 NCBIfam TIGR01740 orotidine-5'-phosphate decarboxylase
9 227 InterPro IPR014732 Orotidine 5'-phosphate decarboxylase
1 232 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 232 InterPro IPR013785 Aldolase-type TIM barrel
7 227 SMART SM00934 OMPdecase_2
7 227 InterPro IPR001754 Orotidine 5'-phosphate decarboxylase domain
5 232 Hamap MF_01200_B Orotidine 5'-phosphate decarboxylase [pyrF].
5 232 InterPro IPR047596 Orotidine 5'-phosphate decarboxylase, bacterial
59 72 ProSitePatterns PS00156 Orotidine 5'-phosphate decarboxylase active site.
59 72 InterPro IPR018089 Orotidine 5'-phosphate decarboxylase, active site
2 232 FunFam G3DSA:3.20.20.70:FF:000015 Orotidine 5'-phosphate decarboxylase
6 226 Pfam PF00215 Orotidine 5'-phosphate decarboxylase / HUMPS family
6 226 InterPro IPR001754 Orotidine 5'-phosphate decarboxylase domain
5 230 SUPERFAMILY SSF51366 Ribulose-phoshate binding barrel
5 230 InterPro IPR011060 Ribulose-phosphate binding barrel

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 PA2876
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 0.758

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.

55 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
BMP
1JJK
P08244 340.2 Da LogP -3.03 TPSA 191.5 1 viol. ✓ Clean C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
BMQ
1EIX
P08244 340.2 Da LogP -2.99 TPSA 182.9 ✓ Ro5 ✓ Clean C1C(=O)NC(=O)N(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O…
DTT
2CZD
O58462 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
XMP
2CZF
O58462 365.2 Da LogP -3.44 TPSA 201.2 1 viol. ✓ Clean c1[nH+]c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=…
XPE
3UWQ
Q9KQT7 458.5 Da LogP -0.88 TPSA 123.5 1 viol. ✓ Clean C(COCCOCCOCCOCCOCCOCCOCCOCCOCCO)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.