Overview
Basic information about this protein and its source genome.
- Accession
- PA4985
- Gene
- PA4985
- Status
- annotated
- Amino acids
- 363
- Structure source
- 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.
MNRSFPLRRAASARPHPVFPCRVLLGAVLLAFGGLAPVQADDGLVVVGYGGAGQKAQEVAFFQPFTQQTGIPVVQSEYNGEMARIKVMADTGHADWDLVQVEGPDLARGCDDGLFERLDWQAIGGKQQLIANAAQECGSAALVWGVAIGYDADRLQQPPASWADFWDVQRFPGKRGLRKRAIYNLEFALLADGVPREQVYPLLATRAGADRAFAKLGQLKPYIQWWEAGAQPAQWLAAGDVVMTSTYTGRIADAHRAGRNLALVWQGSLYGMDYWAVVKGSKRGAEARRFIAFANAPDAQVRYVENIPYGPTNRQAAQRLPAQLASWVPTAPANLEQGLAMDDEFWVEHGEELEERFNAWASQ
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
4- GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
- GO:0019810 Binding to putrescine, 1,4-diaminobutane, the polyamine formed by decarboxylation of ornithine and the metabolic precursor of spermidine and spermine.
- GO:0019809 Binding to spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
- GO:0015847 The directed movement of putrescine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Putrescine is 1,4-diaminobutane, the polyamine formed by decarboxylation of ornithine and the metabolic precursor of spermidine and spermine.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 1 | 22 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 23 | 35 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. |
| 41 | 363 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 36 | 40 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 38 | 360 | PANTHER | PTHR30222 | SPERMIDINE/PUTRESCINE-BINDING PERIPLASMIC PROTEIN |
| 44 | 311 | CDD | cd13589 | PBP2_polyamine_RpCGA009 |
| 1 | 40 | SignalP_EUK | SignalP-noTM | SignalP-noTM |
| 48 | 360 | Gene3D | G3DSA:3.40.190.10 | - |
| 145 | 270 | Gene3D | G3DSA:3.40.190.10 | - |
| 62 | 327 | Pfam | PF13416 | Bacterial extracellular solute-binding protein |
| 62 | 327 | InterPro | IPR006059 | Bacterial extracellular solute-binding protein |
| 1 | 40 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM |
| 1 | 40 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 44 | 360 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II |
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
0 + 1Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
PA4985
|
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 |
|---|---|---|---|---|---|---|---|
| 5 | 0.704 | ||||||
| 2 | 0.617 | ||||||
| 3 | 0.411 |
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 |
|---|---|---|---|---|---|---|
| ABU | A9CGA5 | 103.1 Da LogP -0.19 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
C(CC(=O)O)CN
|
|
| MLT | Q89F76 | 134.1 Da LogP -1.09 TPSA 94.8 | ✓ Ro5 | ✓ Clean |
C([C@H](C(=O)O)O)C(=O)O
|
|
| N72 | Q44384 | 309.3 Da LogP -3.46 TPSA 184.6 | 1 viol. | ✓ Clean |
C(CC(=O)O)[C@H](C(=O)O)NCC(=O)[C@@H]([C@@H]([C@…
|
|
| N7T | Q44384 | 309.3 Da LogP -3.46 TPSA 184.6 | 1 viol. | ✓ Clean |
C(CC(=O)O)[C@@H](C(=O)O)NCC(=O)[C@H]([C@@H]([C@…
|
|
| SPD | P0AFK9 | 145.2 Da LogP -0.34 TPSA 64.1 | ✓ Ro5 | ✓ Clean |
C(CCNCCCN)CN
|
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 |
|---|---|---|---|---|---|
| ZINC79036671 | 1.000 | 309.3 Da LogP -3.46 TPSA 184.6 | 1 viol. | ✓ Clean |
O=C(O)CC[C@H](NCC(=O)[C@@H](O)[C@H](O)[C@H](O)C…
|
| ZINC27564039 | 0.933 | 202.3 Da LogP -0.36 TPSA 76.1 | ✓ Ro5 | ✓ Clean |
NCCCCNCCCNCCCN
|
| ZINC13377742 | 0.929 | 230.4 Da LogP 0.42 TPSA 76.1 | ✓ Ro5 | ✓ Clean |
NCCCCNCCCCNCCCCN
|
| ZINC1532734 | 0.929 | 202.3 Da LogP -0.36 TPSA 76.1 | ✓ Ro5 | ✓ Clean |
NCCCNCCCCNCCCN
|
| ZINC1598087 | 0.867 | 215.4 Da LogP 1.61 TPSA 64.1 | ✓ Ro5 | ✓ Clean |
NCCCCCCNCCCCCCN
|
| ZINC13357569 | 0.778 | 243.4 Da LogP 3.71 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCCCC(=O)O
|
| ZINC1763117 | 0.778 | 201.3 Da LogP 2.54 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCC(=O)O
|
| ZINC1845814 | 0.778 | 215.3 Da LogP 2.93 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCC(=O)O
|
| ZINC22048354 | 0.778 | 229.4 Da LogP 3.32 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCCC(=O)O
|
| ZINC34552398 | 0.778 | 257.4 Da LogP 4.10 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCCCCC(=O)O
|
| ZINC34628306 | 0.778 | 271.4 Da LogP 4.49 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCCCCCC(=O)O
|
| ZINC216723569 | 0.675 | 308.3 Da LogP -3.20 TPSA 173.3 | 1 viol. | ✓ Clean |
NCCCC[C@H](NCC(=O)[C@@H](O)[C@H](O)[C@H](O)CO)C…
|
| ZINC3074822 | 0.667 | 229.3 Da LogP 2.11 TPSA 80.4 | ✓ Ro5 | ✓ Clean |
NCCCCCC(=O)CCCCCC(=O)O
|
| ZINC4822737 | 0.667 | 313.5 Da LogP 4.45 TPSA 80.4 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCC(=O)CCCCCC(=O)O
|
| ZINC71773889 | 0.667 | 206.1 Da LogP -1.77 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(C[C@H](O)C(=O)O)C[C@H](O)C(=O)O
|
| ZINC71773890 | 0.667 | 206.1 Da LogP -1.77 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(C[C@H](O)C(=O)O)C[C@@H](O)C(=O)O
|
| ZINC71773891 | 0.667 | 206.1 Da LogP -1.77 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(C[C@@H](O)C(=O)O)C[C@@H](O)C(=O)O
|
| ZINC100056474 | 0.650 | 270.5 Da LogP 4.63 TPSA 38.0 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCCNCCCN
|
| ZINC107767463 | 0.650 | 200.4 Da LogP 2.68 TPSA 38.0 | ✓ Ro5 | ✓ Clean |
CCCCCCNCCCCCCN
|
| ZINC59496006 | 0.650 | 242.5 Da LogP 3.85 TPSA 38.0 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCNCCCN
|
| ZINC2382315668 | 0.614 | 336.3 Da LogP -4.06 TPSA 209.2 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](NCC(=O)[C@@H](O)[C@H](O)[C@H](O…
|
| ZINC2382315669 | 0.614 | 336.3 Da LogP -4.06 TPSA 209.2 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@@H](NCC(=O)[C@@H](O)[C@H](O)[C@H](…
|
| ZINC65742763 | 0.600 | 325.3 Da LogP -4.14 TPSA 204.8 | 1 viol. | ✓ Clean |
O=C(O)CC[C@H](NC(=O)[C@H](O)[C@@H](O)[C@H](O)[C…
|
| ZINC1529497 | 0.588 | 230.3 Da LogP 3.06 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCC(=O)O
|
| ZINC1531045 | 0.588 | 202.2 Da LogP 2.28 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCC(=O)O
|
| ZINC1593115 | 0.588 | 216.3 Da LogP 2.67 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCC(=O)O
|
| ZINC1700020 | 0.588 | 244.3 Da LogP 3.45 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCC(=O)O
|
| ZINC3860440 | 0.588 | 258.4 Da LogP 3.84 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCC(=O)O
|
| ZINC3861298 | 0.588 | 286.4 Da LogP 4.62 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCCCC(=O)O
|
| ZINC5113062 | 0.588 | 272.4 Da LogP 4.23 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCCC(=O)O
|
| ZINC40470158 | 0.577 | 216.3 Da LogP 0.49 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
NCCCC(=O)NCCCCCC(=O)O
|
| ZINC85590372 | 0.575 | 279.3 Da LogP -2.67 TPSA 147.3 | 1 viol. | ✓ Clean |
CC(C)[C@H](NCC(=O)[C@@H](O)[C@H](O)[C@H](O)CO)C…
|
| ZINC78311249 | 0.565 | 203.3 Da LogP -0.54 TPSA 92.6 | ✓ Ro5 | ✓ Clean |
NCCCN(CCCN)CCC(=O)O
|
| ZINC22465713 | 0.563 | 232.4 Da LogP -2.74 TPSA 100.2 | 1 viol. | ✓ Clean |
NCCNCCNCCNCCNCCN
|
| ZINC13433578 | 0.550 | 201.3 Da LogP 1.68 TPSA 80.4 | ✓ Ro5 | ✓ Clean |
NC(=O)CCCCCCCCC(=O)O
|
| ZINC31361891 | 0.550 | 200.3 Da LogP -0.58 TPSA 76.1 | ✓ Ro5 | ✓ Clean |
NCCCNC/C=C/CNCCCN
|
| ZINC4978005 | 0.550 | 200.3 Da LogP -0.58 TPSA 76.1 | ✓ Ro5 | ✓ Clean |
NCCCNC/C=C\CNCCCN
|
| ZINC169723055 | 0.542 | 228.3 Da LogP 1.00 TPSA 98.8 | ✓ Ro5 | Alert |
[N-]=[N+]=NCCCNCCCCNCCCN
|
| ZINC201768036 | 0.542 | 279.3 Da LogP -0.12 TPSA 100.2 | ✓ Ro5 | ✓ Clean |
NCCOCCOCCOCCOCCCC(=O)O
|
| ZINC1577651 | 0.526 | 234.2 Da LogP -0.66 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C[C@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O
|
| ZINC1577652 | 0.526 | 234.2 Da LogP -0.66 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C[C@@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O
|
| ZINC1577653 | 0.526 | 234.2 Da LogP -0.66 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C[C@H](C(=O)O)[C@H](CC(=O)O)C(=O)O
|
| ZINC1703342 | 0.526 | 202.2 Da LogP 1.07 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCC(=O)CCCC(=O)O
|
| ZINC2508031 | 0.526 | 230.3 Da LogP 1.85 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCC(=O)CCCCC(=O)O
|
| ZINC100638283 | 0.524 | 200.4 Da LogP 2.68 TPSA 38.0 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCNCCN
|
| ZINC100967545 | 0.524 | 256.5 Da LogP 4.24 TPSA 38.0 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCCNCCN
|
| ZINC1857785994 | 0.520 | 271.5 Da LogP -0.33 TPSA 70.5 | ✓ Ro5 | ✓ Clean |
NCCCCNCCN1CCN(CCCCN)CC1
|
| ZINC3870097 | 0.520 | 244.4 Da LogP -0.18 TPSA 79.2 | ✓ Ro5 | ✓ Clean |
CC(=O)NCCCNCCCCNCCCN
|
| ZINC4822900 | 0.500 | 300.4 Da LogP 3.80 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCC(=O)CCCCCC(=O)O
|
| ZINC82505156 | 0.500 | 215.3 Da LogP -0.57 TPSA 69.8 | ✓ Ro5 | ✓ Clean |
NCCCN1CCN(CCC(=O)O)CC1
|
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.