Protein profile

VK055_2269

phosphonate ABC transporter, periplasmic phosphonate binding protein

Genome: KpATCC43816

Gene: phnD AIK80874.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GNU5
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Amino acids 308
Annotations 3
Features 18
PDB binders 6
Druggability 0.848

Overview

Basic information about this protein and its source genome.

Accession
VK055_2269
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
phnD AIK80874.1
Status
annotated
Amino acids
308
Structure source
AlphaFold + ColabFold
GO
GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GO:0015716 The directed movement of phosphonates into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A phosphonate is any salt, anion, or ester of phosphonic acid (HPO(OH)2).

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
Periplasmic
ColabFold pLDDT
93.4

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 0.848
Structure A0A0H3GNU5
Pocket Pocket 1
P2Rank 0.887
Structure A0A0H3GNU5
Pocket Pocket 1
ColabFold model
FPocket 0.807 · Pocket 1
P2Rank 0.898 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 37 / 4744 genomes with a hit
Normalized 0.008

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0015716 The directed movement of phosphonates into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A phosphonate is any salt, anion, or ester of phosphonic acid (HPO(OH)2).

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
117 243 Gene3D G3DSA:3.40.190.10 -
1 23 SignalP_EUK SignalP-noTM SignalP-noTM
31 270 Gene3D G3DSA:3.40.190.10 -
23 308 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
15 304 PANTHER PTHR35841 PHOSPHONATES-BINDING PERIPLASMIC PROTEIN
7 303 NCBIfam TIGR03431 phosphonate ABC transporter substrate-binding protein
7 303 InterPro IPR017797 Phosphonate ABC transporter, substrate-binding protein
1 22 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 22 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
33 284 Pfam PF12974 ABC transporter, phosphonate, periplasmic substrate-binding protein
15 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
7 268 NCBIfam TIGR01098 phosphate/phosphite/phosphonate ABC transporter substrate-binding protein
7 268 InterPro IPR005770 Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein
45 299 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
3 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
25 298 CDD cd01071 PBP2_PhnD_like

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_A0A0H3GNU5
AlphaFold — — full sequence — Viewing
ColabFold VK055_2269
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
1 0.848
17 0.359
6 0.297

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 14.59 0.727

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.

17 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
2PO
5O2J
O69052 80.0 Da LogP -1.90 TPSA 63.2 ✓ Ro5 ✓ Clean [O-]P(=O)[O-]
78T
5LV1
A3PDP9 81.0 Da LogP -1.27 TPSA 60.4 ✓ Ro5 ✓ Clean OP(=O)[O-]
BTB
6GHQ
O69061 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
GB
5O37
O69052 96.0 Da LogP -0.21 TPSA 57.5 ✓ Ro5 ✓ Clean CP(=O)(O)O
HP4
5ME4
O69061 65.0 Da LogP -0.98 TPSA 40.1 ✓ Ro5 ✓ Clean [O-][PH2]=O
P7I
3P7I
Q1R3F7 125.1 Da LogP -0.88 TPSA 83.5 ✓ Ro5 ✓ Clean C(CP(=O)(O)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.