Protein profile

KP13_03308

OprD-like protein

Genome: KpKP13

Gene: oprD AHE45687.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU17
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Amino acids 467
Annotations 7
Features 14
PDB binders 1
Druggability 0.96

Overview

Basic information about this protein and its source genome.

Accession
KP13_03308
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
oprD AHE45687.1
Status
annotated
Amino acids
467
Structure source
AlphaFold + ColabFold
GO
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 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: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: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:0015772 The directed movement of oligosaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oligosaccharides are molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
OuterMembrane
ColabFold pLDDT
93.74

Selected Druggability evidence

AlphaFold / UniProt model

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 0.96
Structure A0A0H3GU17
Pocket Pocket 35
P2Rank 0.942
Structure A0A0H3GU17
Pocket Pocket 1
ColabFold model
FPocket 0.819 · Pocket 17
P2Rank 0.597 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 91 / 4744 genomes with a hit
Normalized 0.019

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • 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: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: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:0015772 The directed movement of oligosaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oligosaccharides are molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
  • GO:0015774 The directed movement of polysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
8 467 FunFam G3DSA:2.40.160.10:FF:000007 Outer membrane protein
1 32 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 32 SignalP_EUK SignalP-noTM SignalP-noTM
10 20 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
5 467 Gene3D G3DSA:2.40.160.10 Porin
5 467 InterPro IPR023614 Porin domain superfamily
1 467 PANTHER PTHR34596 CHITOPORIN
1 467 InterPro IPR005318 Outer membrane porin, bacterial
33 467 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
21 32 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 32 Phobius SIGNAL_PEPTIDE Signal peptide region
33 431 Pfam PF03573 outer membrane porin, OprD family
33 431 InterPro IPR005318 Outer membrane porin, bacterial

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 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GU17
AlphaFold — — full sequence — Viewing
ColabFold KP13_03308
ColabFold — — 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
35 0.96

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 29.13 0.929
2 6.34 0.319
3 2.47 0.068
4 1.57 0.024
5 1.22 0.011

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.

51 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
C8E
2ODJ
P32722 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.