Protein profile

PA0958

porin D

Genome: NC_002516.2

Gene: oprD PA0958 occD1 Structure source: Experimental + AlphaFold UniProt P32722
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Amino acids 443
Annotations 10
Features 14
PDB binders 3
Druggability 0.791

Overview

Basic information about this protein and its source genome.

Accession
PA0958
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
oprD PA0958 occD1
Status
annotated
Amino acids
443
Structure source
Experimental + AlphaFold
EC
3.4.21.-
GO
GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures. GO:0019867 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites. GO:0046930 A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids. GO:0015288 Enables the transfer of substances, sized less than 1000 Da, from one side of a membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria. GO:0008236 Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). GO:0015802 The directed movement of basic amino acids, amino acids with a pH above 7, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
OuterMembrane

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 0.791
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • GO:0019867 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
  • GO:0046930 A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids.
  • GO:0015288 Enables the transfer of substances, sized less than 1000 Da, from one side of a membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
  • GO:0008236 Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
  • GO:0015802 The directed movement of basic amino acids, amino acids with a pH above 7, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0006811 The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
24 443 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
34 442 Pfam PF03573 outer membrane porin, OprD family
34 442 InterPro IPR005318 Outer membrane porin, bacterial
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 23 Phobius SIGNAL_PEPTIDE Signal peptide region
1 23 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
7 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
2 443 PANTHER PTHR34596 CHITOPORIN
2 443 InterPro IPR005318 Outer membrane porin, bacterial
5 443 Gene3D G3DSA:2.40.160.10 Porin
5 443 InterPro IPR023614 Porin domain superfamily
1 25 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
19 23 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
30 443 FunFam G3DSA:2.40.160.10:FF:000008 OprD family porin

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

3 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 3SY7
X-ray 2.15 Å A
94.8% 24-443
PDBe RCSB PDBj File
Viewing
PDB 4FOZ
X-ray 2.40 Å A
94.8% 24-443
PDBe RCSB PDBj File
Loaded
PDB 2ODJ
X-ray 2.90 Å A,B
94.4% 26-443
PDBe RCSB PDBj File
Loaded
AlphaFold PA0958
AlphaFold — — full sequence — Loaded
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 0.791

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 5.57 0.267
2 2.39 0.064
3 2.19 0.052
4 1.66 0.028
5 1.17 0.01

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.

53 records

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
C8E
2ODJ 2.90 Å Open crystal
306.4 Da LogP 2.41 TPSA 57.2 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCOCCO

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.