Protein target profile

PA0285

hypothetical protein

Genome: NC_002516.2

Gene: PA0285 3D evidence: AlphaFold DB model UniProt Q9I6K5
Length 760
Pocket druggability 0.716
Ligand records 54
EC / GO 1 / 7
Target summary

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

4 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
PA0285
Gene
PA0285
Status
annotated
Amino acids
760
3D evidence
AlphaFold DB model

Target profile

Computed evidence for target prioritization.

Human off-target
Hit
Human identity (%)
33.333
Human E-value
5.28e-07
Gut microbiome off-target
Hit
Essential (DEG)
N
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 0.716
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MSPRLSALRLSLAYLAIAIAWAFLSDHLLQNQVQDHDQLVFWMTAKRLFFFAATGLLLYLYLVRQFRRKAQAYDELHGSEQRLNRALEAVRDGLWDWDLVTDRMFVSPGYAALIGLAPEELGDPIETWKKRLHPEEYATVLEAHRNHLQGLTDNLDHIYRLRHKDGDYRWIHSRGRVLRDALGKPLHYTGVARDITLQRLKEDHLRQAAAVFDSTREGVLVTDAQAVIVHVNPSFERITGYRSEDVLGKTPAILRSGRQDQAFYQRLWLALREQDVWSGEIWNRRKSGEIYPQWLHIRAVRNDQGQLTHYVGVFSDLSSIKRSENELDFLAHHDSLTGLPNRVLLRERIEQALENGKDRTVAGALLLIDLDHFKHINDSLGHTTGDMLLKEVSKRLQHQLDERCLLSRLGGDEFAILVENDDPEAVARLSQRILDGFNAPFDIHCQPIYISASLGVSLYPEDASDVDHLMQHADAALFQAKDSGRNAYAFYTRVLTARARAHVQVESALRHALEHDELRVHYQPVHDLASGRIVGVESLVRWQHPERGLVPPGEFVPVAEECGLIAALDNWVLKRACRQMREWQQRGVELEFVAVNVSSRLFNRGGLEERIANALEESGLEPRYLELEVTESAVMEDFEQSLNLLCRLRILGVNLAIDDFGTGYSSLMRLKRLPVHKLKIDQGFVAGLPGAVDDAAIARAIVALAQSMGLRVVAEGIEHQDQALFLREHGCDFGQGYWYGRPQPAEALRFDLPPVALPED

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0061939 Any process that mediates the transfer of information from one cell to another using c-di-GMP as the signal.
  • 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.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0005515 Binding to a protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

70 records
Show feature table
Start End DB Term Name
104 192 InterPro IPR013655 PAS fold-3
87 199 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain)
87 199 InterPro IPR035965 PAS domain superfamily
326 492 FunFam G3DSA:3.30.70.270:FF:000001 Diguanylate cyclase domain protein
331 486 Pfam PF00990 Diguanylate cyclase, GGDEF domain
331 486 InterPro IPR000160 GGDEF domain
215 317 CDD cd00130 PAS
215 317 InterPro IPR000014 PAS domain
325 493 Gene3D G3DSA:3.30.70.270 -
325 493 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
39 61 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
507 742 Pfam PF00563 EAL domain
507 742 InterPro IPR001633 EAL domain
92 195 CDD cd00130 PAS
92 195 InterPro IPR000014 PAS domain
507 747 CDD cd01948 EAL
507 747 InterPro IPR001633 EAL domain
361 493 ProSiteProfiles PS50887 GGDEF domain profile.
361 493 InterPro IPR000160 GGDEF domain
81 149 SMART SM00091 pas_2
81 149 InterPro IPR000014 PAS domain
206 272 SMART SM00091 pas_2
206 272 InterPro IPR000014 PAS domain
209 327 NCBIfam TIGR00229 PAS domain S-box protein
209 327 InterPro IPR000014 PAS domain
79 197 NCBIfam TIGR00229 PAS domain S-box protein
79 197 InterPro IPR000014 PAS domain
502 752 FunFam G3DSA:3.20.20.450:FF:000001 Cyclic di-GMP phosphodiesterase yahA
502 756 ProSiteProfiles PS50883 EAL domain profile.
502 756 InterPro IPR001633 EAL domain
44 63 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
277 329 ProSiteProfiles PS50113 PAC domain profile.
277 329 InterPro IPR000700 PAS-associated, C-terminal
209 316 Pfam PF00989 PAS fold
209 316 InterPro IPR013767 PAS fold
199 324 Gene3D G3DSA:3.30.450.20 PAS domain
506 749 SUPERFAMILY SSF141868 EAL domain-like
506 749 InterPro IPR035919 EAL domain superfamily
502 752 Gene3D G3DSA:3.20.20.450 EAL domain
502 752 InterPro IPR035919 EAL domain superfamily
336 492 SUPERFAMILY SSF55073 Nucleotide cyclase
336 492 InterPro IPR029787 Nucleotide cyclase
64 760 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
204 250 ProSiteProfiles PS50112 PAS repeat profile.
204 250 InterPro IPR000014 PAS domain
327 489 NCBIfam TIGR00254 diguanylate cyclase (GGDEF) domain
327 489 InterPro IPR000160 GGDEF domain
1 6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
156 198 SMART SM00086 pac_2
156 198 InterPro IPR001610 PAC motif
278 320 SMART SM00086 pac_2
278 320 InterPro IPR001610 PAC motif
5 24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 24 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
501 747 SMART SM00052 duf2_2
501 747 InterPro IPR001633 EAL domain
155 207 ProSiteProfiles PS50113 PAC domain profile.
155 207 InterPro IPR000700 PAS-associated, C-terminal
104 192 Pfam PF08447 PAS fold
25 43 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
320 491 SMART SM00267 duf1_3
320 491 InterPro IPR000160 GGDEF domain
74 194 Gene3D G3DSA:3.30.450.20 PAS domain
332 489 CDD cd01949 GGDEF
332 489 InterPro IPR000160 GGDEF domain
211 318 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain)
211 318 InterPro IPR035965 PAS domain superfamily
202 748 PANTHER PTHR44757 DIGUANYLATE CYCLASE DGCP
79 151 ProSiteProfiles PS50112 PAS repeat profile.
79 151 InterPro IPR000014 PAS domain

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 PA0285
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 #2
0.716
Show in viewer
Site 2 FPocket #16
0.618
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Site 3 FPocket #14
0.43
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Site 4 FPocket #10
0.218
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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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 54 via homologs
Structural ligands 4 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 53 0 PAINS alerts
Best available ligand signal
C2E PDB via homolog 690.4 Da · LogP -3.05 · TPSA 349.6 Open detail RCSB PDB
Detail RCSB PDB C2E PDB via homolog
Detail RCSB PDB DAO PDB via homolog
Detail RCSB PDB GEY PDB via homolog
Detail RCSB PDB OXY PDB via homolog

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
C2E RCSB PDB Q3SJE6 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…
DAO RCSB PDB C9XTL5 200.3 Da LogP 3.99 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCC(=O)O
GEY RCSB PDB C9XTL5 198.3 Da LogP 3.77 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCC/C=C\C(=O)O
OXY RCSB PDB P76129 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean 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.