Protein profile

PA1056

monovalent cation/H+ antiporter subunit D

Genome: NC_002516.2

Gene: PA1056 Structure source: AlphaFold UniProt Q9I4R8
Amino acids 499
Annotations 5
Features 54
PDB binders 11
Druggability 0.816

Overview

Basic information about this protein and its source genome.

Accession
PA1056
Gene
PA1056
Status
annotated
Amino acids
499
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
24.803
Human E-value
2.92e-08
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
CytoplasmicMembrane

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.816
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

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:0008137 Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) = NAD+ + ubiquinol + 4 H+(out).
  • GO:0015385 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Na+(out) + H+(in) = Na+(in) + H+(out).
  • GO:0042773 The transfer of electrons through a series of electron donors and acceptors, generating energy that is ultimately used for synthesis of ATP.
  • GO:0035725 A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

54 records
Show feature table
Start End DB Term Name
76 98 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
256 274 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
235 255 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
450 469 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
324 346 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
105 122 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
106 123 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
295 300 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
409 429 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
52 62 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
95 105 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
229 234 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
450 469 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
301 319 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
63 94 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
124 128 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
25 30 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
160 182 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
6 24 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
377 403 PRINTS PR01437 NADH-ubiquinone oxidoreductase subunit 4 signature
377 403 InterPro IPR003918 NADH:ubiquinone oxidoreductase
159 183 PRINTS PR01437 NADH-ubiquinone oxidoreductase subunit 4 signature
159 183 InterPro IPR003918 NADH:ubiquinone oxidoreductase
129 148 PRINTS PR01437 NADH-ubiquinone oxidoreductase subunit 4 signature
129 148 InterPro IPR003918 NADH:ubiquinone oxidoreductase
232 256 PRINTS PR01437 NADH-ubiquinone oxidoreductase subunit 4 signature
232 256 InterPro IPR003918 NADH:ubiquinone oxidoreductase
201 228 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
470 499 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
430 449 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
320 330 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
272 294 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
124 417 Pfam PF00361 Proton-conducting membrane transporter
124 417 InterPro IPR001750 NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit
371 389 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
390 408 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
148 158 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
30 52 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
408 430 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 493 PANTHER PTHR42703 NADH DEHYDROGENASE
159 181 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
31 51 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
351 370 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
331 350 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
126 148 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
206 228 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
371 393 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
182 200 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4 23 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
129 147 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
301 320 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
275 294 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
235 257 TMHMM TMhelix 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; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA1056
AlphaFold 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 0.712
20 0.462
21 0.261
4 0.248

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.

61 records

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
BCR Q8DMR6 536.9 Da LogP 12.61 TPSA 0.0 2 viol. ✓ Clean CC1=C(C(CCC1)(C)C)\C=C\C(=C\C=C\C(=C\C=C\C=C(/C…
DGD Q8DMR6 949.3 Da LogP 7.61 TPSA 231.1 4 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C…
FES Q8DMR6 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
LHG Q8DMR6 723.0 Da LogP 9.89 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@…
LMG Q8DMR6 787.2 Da LogP 9.78 TPSA 152.0 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C…
LMT A0A221C8X0 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
PGT Q8DMR6 751.0 Da LogP 10.67 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)O[C@@H](COC(=O)CCCCCCCCCC…
PL9 Q8DMR6 749.2 Da LogP 16.57 TPSA 34.1 2 viol. Alert CC1=C(C(=O)C(=CC1=O)CC=C(C)CCC=C(C)CCC=C(C)CCC=…
PQN Q8DMR6 450.7 Da LogP 9.16 TPSA 34.1 1 viol. Alert CC1=C(C(=O)c2ccccc2C1=O)C\C=C(/C)\CCC[C@H](C)CC…
PTY B7GL84 734.1 Da LogP 11.67 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC…
SQD Q8DMR6 795.1 Da LogP 8.12 TPSA 186.1 3 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](COC1[C@@H]([C@H]([C…

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.