Protein target profile

PA4670

ribose-phosphate pyrophosphokinase

Genome: NC_002516.2

Gene: prs PA4670 3D evidence: AlphaFold DB model UniProt Q9HVC5
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Length 313
Pocket druggability 0.71
Ligand records 52
EC / GO 1 / 11
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

4 signals

Strengths

Strong predicted binding pocket FPocket selected-pocket score 0.71. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model Ligand evidence via structure/bioactivity 2 structural and 0 bioactivity records.

Risks / watch

Human similarity Top human hit identity: 56.452%.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
How to read this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal TPW pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Overview

Basic information about this protein and its source genome.

Accession
PA4670
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
prs PA4670
Status
annotated
Amino acids
313
3D evidence
AlphaFold DB model
EC
2.7.6.1
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0002189 A protein complex having ribose phosphate diphosphokinase activity. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GO:0000287 Binding to a magnesium (Mg) ion. GO:0004749 Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 2 H+.

Target profile

Computed evidence for target prioritization.

Human off-target
Hit
Human identity (%)
56.452
Human E-value
2.71e-19
Gut microbiome off-target
Hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected pocket evidence

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.71
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MSKMMVFTGNANPDLARRVVRQLHIPLGDVSVGKFSDGEISVEINENVRGKDVFLIQPTCAPTNDNLMELVVMADAFRRSSATRITAVIPYFGYARQDRRPRSARVAISAKVVADMLTVVGVNRVLTVDLHADQIQGFFDIPVDNIYGSPVLVDDIEDQRFENLMIVSPDIGGVVRARAVAKSLGVDLAIIDKRRPKANQSEVMHIIGDVEGRTCVLVDDMVDTAGTLGHAAKALKEHGAAKVIAYCTHPVLSGRAIENIEKSVLDELVVTNTIPLSAAAQACGRIRQLDIAPVVAEAMRRISNEESISAMFR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0002189 A protein complex having ribose phosphate diphosphokinase activity.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0004749 Catalysis of the reaction: D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + 2 H+.
  • GO:0006015 The chemical reactions and pathways resulting in the formation of 5-phosphoribose 1-diphosphate, also known as 5-phosphoribosyl-1-pyrophosphate.
  • GO:0006164 The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
  • GO:0009156 The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
  • GO:0044249 OBSOLETE. The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
  • GO:0009165 The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
7 160 FunFam G3DSA:3.40.50.2020:FF:000001 Ribose-phosphate pyrophosphokinase
4 313 NCBIfam TIGR01251 ribose-phosphate diphosphokinase
4 313 InterPro IPR005946 Ribose-phosphate pyrophosphokinase
69 305 SUPERFAMILY SSF53271 PRTase-like
69 305 InterPro IPR029057 Phosphoribosyltransferase-like
7 304 Gene3D G3DSA:3.40.50.2020 -
7 304 InterPro IPR029057 Phosphoribosyltransferase-like
4 121 Pfam PF13793 N-terminal domain of ribose phosphate pyrophosphokinase
4 121 InterPro IPR029099 Ribose-phosphate pyrophosphokinase, N-terminal domain
201 313 Pfam PF14572 Phosphoribosyl synthetase-associated domain
201 313 InterPro IPR005946 Ribose-phosphate pyrophosphokinase
4 121 SMART SM01400 Pribosyltran_N_2
4 313 Hamap MF_00583_B Putative ribose-phosphate pyrophosphokinase [prs].
4 313 InterPro IPR037515 Ribose-phosphate pyrophosphokinase, bacterial-type
148 289 Gene3D G3DSA:3.40.50.2020 -
148 289 InterPro IPR029057 Phosphoribosyltransferase-like
1 313 PANTHER PTHR10210 RIBOSE-PHOSPHATE DIPHOSPHOKINASE FAMILY MEMBER
1 313 InterPro IPR005946 Ribose-phosphate pyrophosphokinase
149 273 CDD cd06223 PRTases_typeI
149 273 InterPro IPR000836 Phosphoribosyltransferase domain
129 144 ProSitePatterns PS00114 Phosphoribosyl pyrophosphate synthase signature.
129 144 InterPro IPR000842 Phosphoribosyl pyrophosphate synthetase, conserved site

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

3D visualization script Full viewer

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Structural evidence

0 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB PA4670
AlphaFold DB — — full sequence — Viewing
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.71
Show in viewer

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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 52 via homologs
Structural ligands 2 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 22 0 PAINS alerts
Best available ligand signal
APC PDB via homolog 505.2 Da · LogP -1.52 · TPSA 269.9 Open detail RCSB PDB
Detail RCSB PDB APC PDB via homolog
Detail RCSB PDB R5P PDB via homolog
Detail ZINC ZINC1530556 ZINC proposed compound · Tanimoto 1.000
Detail ZINC ZINC22116391 ZINC proposed compound · Tanimoto 1.000

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
APC RCSB PDB
3LPN
Q97CA5 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
R5P RCSB PDB
1U9Z
Q58761 230.1 Da LogP -2.62 TPSA 144.5 ✓ Ro5 ✓ Clean C(C(C(C(C=O)O)O)O)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.