Protein profile
PA3383
phosphonate ABC transporter substrate-binding protein
Genome: NC_002516.2
Overview
Basic information about this protein and its source genome.
- Accession
- PA3383
- Gene
- PA3383
- Status
- annotated
- Amino acids
- 334
- Structure source
- Experimental + AlphaFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- No hit
- Gut microbiome off-target
- hit
- Essential (DEG)
- N
- Localization
- Periplasmic
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.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
4- 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:0030313 An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present.
- 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).
- GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 301 | 328 | Coils | Coil | Coil |
| 1 | 7 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 115 | 227 | Gene3D | G3DSA:3.40.190.10 | - |
| 26 | 334 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 7 | 252 | NCBIfam | TIGR01098 | phosphate/phosphite/phosphonate ABC transporter substrate-binding protein |
| 7 | 252 | InterPro | IPR005770 | Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein |
| 49 | 243 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II |
| 121 | 141 | Coils | Coil | Coil |
| 25 | 282 | CDD | cd13575 | PBP2_PnhD |
| 2 | 289 | NCBIfam | TIGR03431 | phosphonate ABC transporter substrate-binding protein |
| 2 | 289 | InterPro | IPR017797 | Phosphonate ABC transporter, substrate-binding protein |
| 1 | 25 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM |
| 20 | 25 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 1 | 25 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM |
| 275 | 334 | Gene3D | G3DSA:1.20.58.90 | - |
| 30 | 262 | Gene3D | G3DSA:3.40.190.10 | - |
| 3 | 334 | PANTHER | PTHR30043 | PHOSPHONATES TRANSPORT SYSTEM PERMEASE PROTEIN |
| 32 | 277 | Pfam | PF12974 | ABC transporter, phosphonate, periplasmic substrate-binding protein |
| 8 | 19 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. |
| 1 | 25 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
3D Structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.
Loading 3D structure...
Structural evidence
1 + 1Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
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 | 0.614 | ||||||
| 3 | 0.291 |
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 | 14.19 | 0.714 | ||||||
| 2 | 4.5 | 0.192 | ||||||
| 3 | 3.19 | 0.109 | ||||||
| 4 | 1.21 | 0.011 | ||||||
| 5 | 0.68 | 0.001 |
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 | 0.725 |
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.
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.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| 2PO | O69052 | 80.0 Da LogP -1.90 TPSA 63.2 | ✓ Ro5 | ✓ Clean |
[O-]P(=O)[O-]
|
|
| 78T | A3PDP9 | 81.0 Da LogP -1.27 TPSA 60.4 | ✓ Ro5 | ✓ Clean |
OP(=O)[O-]
|
|
| BTB | O69061 | 209.2 Da LogP -3.01 TPSA 104.4 | ✓ Ro5 | ✓ Clean |
C(CO)N(CCO)C(CO)(CO)CO
|
|
| GB | A3PC74 | 96.0 Da LogP -0.21 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
CP(=O)(O)O
|
|
| HP4 | O69061 | 65.0 Da LogP -0.98 TPSA 40.1 | ✓ Ro5 | ✓ Clean |
[O-][PH2]=O
|
|
| P7I | Q1R3F7 | 125.1 Da LogP -0.88 TPSA 83.5 | ✓ Ro5 | ✓ Clean |
C(CP(=O)(O)O)N
|
|
| PO3 | A3PC74 | 79.0 Da LogP -1.64 TPSA 63.2 | ✓ Ro5 | ✓ Clean |
[O-][P-](=O)[O-]
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC1615342 | 1.000 | 209.2 Da LogP -3.01 TPSA 104.4 | ✓ Ro5 | ✓ Clean |
OCCN(CCO)C(CO)(CO)CO
|
| ZINC96639846 | 0.600 | 265.3 Da LogP 3.02 TPSA 83.6 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCCP(=O)(O)O
|
| ZINC2381636 | 0.529 | 218.1 Da LogP 0.12 TPSA 115.1 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)CCCCP(=O)(O)O
|
| ZINC31962397 | 0.529 | 204.1 Da LogP -0.27 TPSA 115.1 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)CCCP(=O)(O)O
|
| ZINC2334905 | 0.522 | 261.4 Da LogP 1.10 TPSA 63.9 | ✓ Ro5 | ✓ Clean |
CC(C)CCN(CCC(C)C)C(CO)(CO)CO
|
| ZINC3159953 | 0.522 | 261.4 Da LogP 1.38 TPSA 63.9 | ✓ Ro5 | ✓ Clean |
CCCCCN(CCCCC)C(CO)(CO)CO
|
| ZINC2381412 | 0.500 | 246.1 Da LogP 0.90 TPSA 115.1 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)CCCCCCP(=O)(O)O
|
| ZINC2569998 | 0.500 | 232.1 Da LogP 0.51 TPSA 115.1 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)CCCCCP(=O)(O)O
|
| ZINC34227522 | 0.500 | 302.2 Da LogP 2.46 TPSA 115.1 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)CCCCCCCCCCP(=O)(O)O
|
| ZINC34744001 | 0.500 | 274.2 Da LogP 1.68 TPSA 115.1 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)CCCCCCCCP(=O)(O)O
|
| ZINC38594934 | 0.500 | 330.3 Da LogP 3.24 TPSA 115.1 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)CCCCCCCCCCCCP(=O)(O)O
|
| ZINC5297554 | 0.500 | 289.5 Da LogP 2.16 TPSA 63.9 | ✓ Ro5 | ✓ Clean |
CCCCCCN(CCCCCC)C(CO)(CO)CO
|
| ZINC97941822 | 0.500 | 317.5 Da LogP 2.94 TPSA 63.9 | ✓ Ro5 | ✓ Clean |
CCCCCCCN(CCCCCCC)C(CO)(CO)CO
|
| ZINC97942927 | 0.500 | 373.6 Da LogP 4.51 TPSA 63.9 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCN(CCCCCCCCC)C(CO)(CO)CO
|
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.