Protein target profile

PA1727

signaling protein

Genome: NC_002516.2

Gene: PA1727 mucR 3D evidence: Experimental + AlphaFold DB model UniProt Q9I310
Length 685
Pocket druggability 0.722
Ligand records 51
EC / GO 2 / 5
Target summary

Promising target candidate with multiple supporting evidence streams.

6 signals
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
PA1727
Gene
PA1727 mucR
Status
annotated
Amino acids
685
3D evidence
Experimental + AlphaFold DB model

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
Hit
Essential (DEG)
Y
Localization
CytoplasmicMembrane

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 0.722
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MLISSYNQVLVAFSLIVAILASYTALDMAGRVTLAKGREALSWLIGGAFAMGFGIWSMHFVGMLAFSLPIPLGYDLGLTLLSLLLAVGSSAFALWLVCQAELPWQRLALGALLMGSGIAAMHYTGMAALLMMPGIVYDPLWLGLSILIAVIASGAALWIAFRLRHGSRRIVLVRAGAALVMGCAIVGMHYTGMAAAQFPLGSFCGAAGRGIDNGWLAVLVIVITLAVIAIALIVSVLDSRLEARTSVLATSLARANRELIQLALHDNLTKLPNRMLLDDRLEQAIQQAIRDDRRFAVLFMDLDGFKAVNDAYGHHLGDLLLIEVAERIRANVRAQDTIARLGGDEFVLLIEAREPADAATLAEKLVKRISQPYQISRHEVRISASIGIALYPGDGQTRHELMINADAAMYHAKDQGRNGYCFFESSMNANAQEQLQLLHDLRQALERRQLVLHYQPKVLAPNGPMIGVEALLRWEHPQHGLITPGQFLPLAEKTGLIVQIGEWVLDEACRQMRLWLDGGHADWNIAVNLSALQFAHAGLVDSVRNALLRHSLEPSHLILEVTESTAMRDADASLVILEQLSAMGVGISIDDFGTGYSSLLYLKRLPASELKIDRGFINELAHDSDDAAIVSAIVALGRTLNLKIVAEGVETEAQQEFLTRLGCNSLQGFLLGRPMPAEQLLASVA

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 5 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

5
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0071111 Catalysis of the reaction: cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine + H+.
  • GO:0052621 Catalysis of the reaction: 2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate + 2 H+.
  • GO:0046872 Binding to a metal ion.
  • GO:0071732 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.

Sequence Features

Domain/signature hits from InterPro and related databases.

60 records
Show feature table
Start End DB Term Name
41 66 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
76 98 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
261 421 NCBIfam TIGR00254 diguanylate cyclase (GGDEF) domain
261 421 InterPro IPR000160 GGDEF domain
140 159 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
264 421 CDD cd01949 GGDEF
264 421 InterPro IPR000160 GGDEF domain
268 425 SUPERFAMILY SSF55073 Nucleotide cyclase
268 425 InterPro IPR029787 Nucleotide cyclase
39 61 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
6 199 ProSiteProfiles PS50924 MHYT domain profile.
6 199 InterPro IPR005330 MHYT domain
160 170 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
433 679 SMART SM00052 duf2_2
433 679 InterPro IPR001633 EAL domain
293 425 ProSiteProfiles PS50887 GGDEF domain profile.
293 425 InterPro IPR000160 GGDEF domain
238 685 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
440 674 Pfam PF00563 EAL domain
440 674 InterPro IPR001633 EAL domain
135 139 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
170 192 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
4 26 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
98 108 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
215 237 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
250 682 PANTHER PTHR44757 DIGUANYLATE CYCLASE DGCP
258 436 Gene3D G3DSA:3.30.70.270 -
258 436 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
439 679 CDD cd01948 EAL
439 679 InterPro IPR001633 EAL domain
6 29 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
196 214 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
434 685 ProSiteProfiles PS50883 EAL domain profile.
434 685 InterPro IPR001633 EAL domain
263 418 Pfam PF00990 Diguanylate cyclase, GGDEF domain
263 418 InterPro IPR000160 GGDEF domain
67 77 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
439 682 SUPERFAMILY SSF141868 EAL domain-like
439 682 InterPro IPR035919 EAL domain superfamily
437 685 Gene3D G3DSA:3.20.20.450 EAL domain
437 685 InterPro IPR035919 EAL domain superfamily
78 97 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
428 448 Coils Coil Coil
258 424 FunFam G3DSA:3.30.70.270:FF:000001 Diguanylate cyclase domain protein
252 423 SMART SM00267 duf1_3
252 423 InterPro IPR000160 GGDEF domain
434 685 FunFam G3DSA:3.20.20.450:FF:000001 Cyclic di-GMP phosphodiesterase yahA
215 237 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
107 129 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
115 171 Pfam PF03707 Bacterial signalling protein N terminal repeat
115 171 InterPro IPR005330 MHYT domain
52 109 Pfam PF03707 Bacterial signalling protein N terminal repeat
52 109 InterPro IPR005330 MHYT domain
182 245 Pfam PF03707 Bacterial signalling protein N terminal repeat
182 245 InterPro IPR005330 MHYT domain
139 161 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
171 195 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
30 40 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
109 134 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

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

1 + 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
PDB 5M1T
X-ray 2.27 Å A,B
38.0% 426-685
Viewing
AlphaFold DB PA1727
AlphaFold DB full sequence Loaded
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
0.722
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Site 2 FPocket #2
0.289
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Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.464
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Site 2 P2Rank #2
0.345
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Site 3 P2Rank #3
0.143
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Site 4 P2Rank #4
0.062
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Site 5 P2Rank #5
0.059
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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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 1 50 via homologs
Structural ligands 1 1 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 47 0 PAINS alerts
Best available ligand signal
C2E PDB co-crystal 690.4 Da · LogP -3.05 · TPSA 349.6 Open detail RCSB PDB
Detail RCSB PDB C2E PDB co-crystal
Detail ZINC ZINC12501894 ZINC proposed compound · Tanimoto 1.000
Detail ZINC ZINC33494013 ZINC proposed compound · Tanimoto 1.000
Detail ZINC ZINC4095501 ZINC proposed compound · Tanimoto 1.000

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
C2E RCSB PDB 690.4 Da LogP -3.05 TPSA 349.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@H]4[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.