Protein target profile

PA4843

two-component response regulator

Genome: NC_002516.2

Gene: PA4843 3D evidence: AlphaFold DB model UniProt Q9HUW7
Length 542
Pocket druggability 0.695
Ligand records 54
EC / GO 1 / 8
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
PA4843
Gene
PA4843
Status
annotated
Amino acids
542
3D evidence
AlphaFold DB model

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
Hit
Essential (DEG)
N
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 0.695
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MMTEHDDPTLDRLKHHFAQRVINQARQVLEVWQRLTRAEWNSDGMEELADATLRLQRYAERFEQAEHAQLAGAIDRTLDVVEANRGRLSSESISELNQLMQRLSRTGLRHGDQLEHTVLPPLRKPVYLALKDRERAERLAQQLEFFGLQALSCETADAFRASMRERYPAAIVMEVDFAGPDMGLRLASEAQAGLEHKLPVLFFSDSETDTPTRLAAARAGGQEFFTGTLDASSVLEKIETLSRLSFYEPYRVLIVDDSRAQALHTEMVLNSAGIITRALTEPLSVMAELSDFQPDLIILDMYMPECLGTELAKVIRQHERHVSVPIIYLSAEDDLDKQLDAMSEGGDDFLTKPIRPRHLIATVRTRASRARSLKARMVRDSLTGLYNHTHTLQLLEDARLRARRDGRPLSFAMLDIDHFKQVNDRFGHPMGDRVIKGLALFLKQRLRKTDHIGRYGGEEFAVVLPDTDLDAARLVLDEIRQRFAEIHYPAQPTDLRCTFSCGIAELTPDLDIKSMAKQADEALYRAKHGGRNRIEVYRPDAR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • 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:0052621 Catalysis of the reaction: 2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate + 2 H+.
  • GO:0043709 The attachment of a cell to a solid substrate, via cell adhesion molecules, during the formation of a biofilm composed of microorganisms of the same species.
  • GO:1902201 Any process that stops, prevents or reduces the frequency, rate or extent of bacterial-type flagellum-dependent cell motility.
  • GO:0000160 A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
  • GO:1900189 Any process that activates or increases the frequency, rate or extent of cell adhesion involved in single-species biofilm formation.
  • GO:1900233 Any process that activates or increases the frequency, rate or extent of single-species biofilm formation on inanimate substrate.
  • GO:1902065 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an L-glutamate stimulus.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
407 539 ProSiteProfiles PS50887 GGDEF domain profile.
407 539 InterPro IPR000160 GGDEF domain
48 68 Coils Coil Coil
134 243 SUPERFAMILY SSF52172 CheY-like
134 243 InterPro IPR011006 CheY-like superfamily
379 533 Pfam PF00990 Diguanylate cyclase, GGDEF domain
379 533 InterPro IPR000160 GGDEF domain
245 375 Gene3D G3DSA:3.40.50.2300 -
374 536 NCBIfam TIGR00254 diguanylate cyclase (GGDEF) domain
374 536 InterPro IPR000160 GGDEF domain
379 534 CDD cd01949 GGDEF
379 534 InterPro IPR000160 GGDEF domain
247 375 FunFam G3DSA:3.40.50.2300:FF:000346 Diguanylate cyclase response regulator
251 367 ProSiteProfiles PS50110 Response regulatory domain profile.
251 367 InterPro IPR001789 Signal transduction response regulator, receiver domain
366 537 SMART SM00267 duf1_3
366 537 InterPro IPR000160 GGDEF domain
246 378 SUPERFAMILY SSF52172 CheY-like
246 378 InterPro IPR011006 CheY-like superfamily
376 540 Gene3D G3DSA:3.30.70.270 -
376 540 InterPro IPR043128 Reverse transcriptase/Diguanylate cyclase domain
250 363 SMART SM00448 REC_2
250 363 InterPro IPR001789 Signal transduction response regulator, receiver domain
112 243 Gene3D G3DSA:3.40.50.2300 -
253 353 CDD cd00156 REC
372 538 FunFam G3DSA:3.30.70.270:FF:000001 Diguanylate cyclase domain protein
125 242 ProSiteProfiles PS50110 Response regulatory domain profile.
125 242 InterPro IPR001789 Signal transduction response regulator, receiver domain
64 539 PANTHER PTHR45138 REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM
252 363 Pfam PF00072 Response regulator receiver domain
252 363 InterPro IPR001789 Signal transduction response regulator, receiver domain
382 539 SUPERFAMILY SSF55073 Nucleotide cyclase
382 539 InterPro IPR029787 Nucleotide cyclase

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 PA4843
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
0.695
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.

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 40 0 PAINS alerts
Best available ligand signal
BEF PDB via homolog 66.0 Da · LogP 0.88 · TPSA 0.0 Open detail RCSB PDB
Detail RCSB PDB BEF PDB via homolog
Detail RCSB PDB C2E PDB via homolog
Detail RCSB PDB GAV PDB via homolog
Detail RCSB PDB TLA 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
BEF RCSB PDB B8GZM2 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
C2E RCSB PDB A1U3W3 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…
GAV RCSB PDB B8GZM2 539.2 Da LogP -1.40 TPSA 278.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
TLA RCSB PDB Q9HXT9 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=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.