Protein target profile

PA4513

oxidoreductase

Genome: NC_002516.2

Gene: PA4513 3D evidence: AlphaFold DB model UniProt Q9HVQ8
Length 850
Pocket druggability 0.705
Ligand records 55
EC / GO 0 / 6
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
PA4513
Gene
PA4513
Status
annotated
Amino acids
850
3D evidence
AlphaFold DB model

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
34.314
Human E-value
1.61e-09
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 0.705
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MKKVWFQLHWFFGISAGLVLALMGVTGATLSFQDELMRALNPDVLVVQKRPEGVLPLDELVRRIEGAEPGRKVAFVWVEMDSDKAGRIFYTPPPGQRRGESRWIDPYTGAFVGEPRGEGFFNLMMQLHRFLAMGEYGKQVTAACTLILIFFCLSGLYLRWPRKVFDWRAWLTLDWSRKGRSFNWDLHAVAGTWCLALYLLAALTGLYWSYEWYRNGLFKLLDDAPAGQQAQRGKPGGRGERPADAAPLVVDYAAVWNSIRQAGGDRLQAYNLRLPPAGGQPATVFYRLTDAPHERAFNTLTLDPANGQVKSDQRYSDRSFGSQLLASVYALHVGSYFGMAGRILMMLASLAMPLFFITGWLLYLDRRRKKRAVRASRADLGGSAGASGEPWLIGYASQSGFAEQLAWQSAGQLQAAGLPVRVESLARLDAGQLAEARKALFVVSTFGDGEAPDSARGFERKVLGQAASLDGLSYALLALGDRQYEQFCGFARRMQGWLQGQGARSLFAPVEVDDGDAAALRQWQESLAEVTGGAAPAAWEAPAFEVWSLARRECLNPGSQGESTWLLDLRAPANSAIQWRAGDLLEIVPHQAPVRIREWLQRHNLDGQARVAVEGVEQSLEQALAGRLLPDSFEHLVGLHPQALLDALIPLSVRQYSIASLQSDGDLQLIVRQEQHADGSLGICSGWLTEYLPLGAALTLRLRRNAGFHLPEDDVPLILIGNGTGLAGLRSLLRASIAAGRKRNWLLFGERNFAHDYYCRAELEQALARGELQRLDLAFSRDQAEKIYVQDRLHEAADELRRWIDEGAALYVCGSLQGMAGGVDRVLREVLGEEALQRLADEGRYRRDVY

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0016655 Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
  • GO:0071281 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 an iron ion stimulus.

Sequence Features

Domain/signature hits from InterPro and related databases.

60 records
Show feature table
Start End DB Term Name
682 691 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
682 691 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
579 589 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
579 589 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
786 802 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
786 802 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
654 661 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
654 661 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
718 737 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
718 737 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
809 817 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
809 817 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
742 751 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
742 751 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
188 210 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
338 342 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
707 850 SUPERFAMILY SSF52343 Ferredoxin reductase-like, C-terminal NADP-linked domain
707 850 InterPro IPR039261 Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
1 406 PANTHER PTHR34219 IRON-REGULATED INNER MEMBRANE PROTEIN-RELATED
1 406 InterPro IPR005625 PepSY-associated TM protein
10 32 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
471 481 PRINTS PR00369 Flavodoxin signature
471 481 InterPro IPR001094 Flavodoxin-like
392 405 PRINTS PR00369 Flavodoxin signature
392 405 InterPro IPR001094 Flavodoxin-like
440 451 PRINTS PR00369 Flavodoxin signature
440 451 InterPro IPR001094 Flavodoxin-like
211 319 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
547 850 CDD cd06200 SiR_like1
186 210 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
393 522 Pfam PF00258 Flavodoxin
393 522 InterPro IPR008254 Flavodoxin/nitric oxide synthase
140 160 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
320 337 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
539 709 SUPERFAMILY SSF63380 Riboflavin synthase domain-like
539 709 InterPro IPR017938 Riboflavin synthase-like beta-barrel
364 534 Gene3D G3DSA:3.40.50.360 -
364 534 InterPro IPR029039 Flavoprotein-like superfamily
161 185 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
719 823 Pfam PF00175 Oxidoreductase NAD-binding domain
719 823 InterPro IPR001433 Oxidoreductase FAD/NAD(P)-binding
708 850 Gene3D G3DSA:3.40.50.80 -
708 850 InterPro IPR039261 Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
31 139 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
6 30 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
343 364 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
319 338 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
391 528 ProSiteProfiles PS50902 Flavodoxin-like domain profile.
391 528 InterPro IPR008254 Flavodoxin/nitric oxide synthase
6 366 Pfam PF03929 PepSY-associated TM region
6 366 InterPro IPR005625 PepSY-associated TM protein
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
542 711 ProSiteProfiles PS51384 Ferredoxin reductase-type FAD binding domain profile.
542 711 InterPro IPR017927 FAD-binding domain, ferredoxin reductase-type
365 850 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
139 161 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
342 364 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
388 531 SUPERFAMILY SSF52218 Flavoproteins
388 531 InterPro IPR029039 Flavoprotein-like superfamily
364 534 FunFam G3DSA:3.40.50.360:FF:000070 Bifunctional sulfite reductase [NADPH] flavoprotein alpha-component/iron-uptake factor

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 PA4513
AlphaFold DB 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 0.705

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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 55 via homologs
Structural ligands 5 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 32 1 PAINS alerts
Best available ligand signal
2AM PDB via homolog 347.2 Da · LogP -1.86 · TPSA 186.1 Open detail RCSB PDB
Detail RCSB PDB 2AM PDB via homolog
Detail RCSB PDB A2P PDB via homolog
Detail RCSB PDB CXS PDB via homolog
Detail RCSB PDB FDA 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
2AM RCSB PDB P00388 347.2 Da LogP -1.86 TPSA 186.1 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
A2P RCSB PDB P00455 427.2 Da LogP -1.75 TPSA 232.6 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
CXS RCSB PDB W8SX42 221.3 Da LogP 1.19 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCCS(=O)(=O)O
FDA RCSB PDB B4G043 787.6 Da LogP -1.75 TPSA 363.3 3 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…
NCA RCSB PDB B4G043 122.1 Da LogP 0.18 TPSA 56.0 ✓ Ro5 ✓ Clean c1cc(cnc1)C(=O)N

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.