Overview
Basic information about this protein and its source genome.
- Accession
- PA5278
- Gene
- dapF PA5278
- Status
- annotated
- Amino acids
- 276
- Structure source
- AlphaFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- No hit
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- Localization
- Cytoplasmic
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.
Enzyme Commission (EC)
1Gene Ontology (GO)
4- GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
- GO:0008837 Catalysis of the reaction: LL-2,6-diaminopimelate = meso-2,6-diaminopimelate.
- GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
- GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 3 | 276 | Hamap | MF_00197 | Diaminopimelate epimerase [dapF]. |
| 3 | 276 | InterPro | IPR001653 | Diaminopimelate epimerase, DapF |
| 121 | 263 | FunFam | G3DSA:3.10.310.10:FF:000002 | Diaminopimelate epimerase |
| 3 | 275 | PANTHER | PTHR31689 | DIAMINOPIMELATE EPIMERASE, CHLOROPLASTIC |
| 3 | 275 | InterPro | IPR001653 | Diaminopimelate epimerase, DapF |
| 3 | 276 | SUPERFAMILY | SSF54506 | Diaminopimelate epimerase-like |
| 4 | 274 | NCBIfam | TIGR00652 | diaminopimelate epimerase |
| 4 | 274 | InterPro | IPR001653 | Diaminopimelate epimerase, DapF |
| 117 | 263 | Gene3D | G3DSA:3.10.310.10 | Diaminopimelate Epimerase; Chain A, domain 1 |
| 5 | 125 | Pfam | PF01678 | Diaminopimelate epimerase |
| 5 | 125 | InterPro | IPR001653 | Diaminopimelate epimerase, DapF |
| 154 | 269 | Pfam | PF01678 | Diaminopimelate epimerase |
| 154 | 269 | InterPro | IPR001653 | Diaminopimelate epimerase, DapF |
| 66 | 80 | ProSitePatterns | PS01326 | Diaminopimelate epimerase signature. |
| 66 | 80 | InterPro | IPR018510 | Diaminopimelate epimerase, active site |
| 4 | 272 | Gene3D | G3DSA:3.10.310.10 | Diaminopimelate Epimerase; Chain A, domain 1 |
| 4 | 120 | FunFam | G3DSA:3.10.310.10:FF:000001 | Diaminopimelate epimerase |
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 |
|---|---|---|---|---|---|---|---|
| 7 | 0.401 | ||||||
| 3 | 0.398 | ||||||
| 1 | 0.263 |
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 |
|---|---|---|---|---|---|---|
| API | Q8NP73 | 190.2 Da LogP -1.02 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
|
|
| DTT | P9WP19 | 154.3 Da LogP -0.43 TPSA 40.5 | ✓ Ro5 | ✓ Clean |
C([C@@H]([C@H](CS)O)O)S
|
|
| TLA | P0A6K1 | 150.1 Da LogP -2.12 TPSA 115.1 | ✓ Ro5 | ✓ Clean |
[C@@H]([C@H](C(=O)O)O)(C(=O)O)O
|
|
| ZDP | P44859 | 204.2 Da LogP -0.63 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
C[C@](CCC[C@@H](C(=O)O)N)(C(=O)O)N
|
|
| ZDR | P44859 | 204.2 Da LogP -0.63 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
C[C@@](CCC[C@@H](C(=O)O)N)(C(=O)O)N
|
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 |
|---|---|---|---|---|---|
| ZINC12359024 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O
|
| ZINC13533920 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC1532740 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O
|
| ZINC1549593 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC2013424 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O
|
| ZINC3581021 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC3860635 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC5783661 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O
|
| ZINC6072527 | 0.692 | 210.1 Da LogP -3.40 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O
|
| ZINC1560405156 | 0.588 | 208.1 Da LogP -1.79 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)/C(O)=C(\O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC1560405157 | 0.588 | 208.1 Da LogP -1.79 TPSA 155.5 | 1 viol. | ✓ Clean |
O=C(O)/C(O)=C(/O)[C@H](O)[C@H](O)C(=O)O
|
| ZINC3055005 | 0.577 | 204.2 Da LogP -0.63 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O
|
| ZINC3055007 | 0.577 | 204.2 Da LogP -0.63 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC3055010 | 0.577 | 204.2 Da LogP -0.63 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1555366 | 0.556 | 232.3 Da LogP 0.15 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O
|
| ZINC1555367 | 0.556 | 232.3 Da LogP 0.15 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1555369 | 0.556 | 232.3 Da LogP 0.15 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1720127 | 0.556 | 218.3 Da LogP -0.24 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O
|
| ZINC1720128 | 0.556 | 218.3 Da LogP -0.24 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC1720130 | 0.556 | 218.3 Da LogP -0.24 TPSA 126.6 | ✓ Ro5 | ✓ Clean |
N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O
|
| ZINC100300547 | 0.548 | 215.3 Da LogP 2.93 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCC[C@@](C)(N)C(=O)O
|
| ZINC1652265 | 0.548 | 215.3 Da LogP 2.93 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCC[C@](C)(N)C(=O)O
|
| ZINC1570993 | 0.516 | 215.3 Da LogP 2.93 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCC[C@H](N)C(=O)O
|
| ZINC1570999 | 0.516 | 229.4 Da LogP 3.32 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCC[C@H](N)C(=O)O
|
| ZINC1620974 | 0.516 | 243.4 Da LogP 3.71 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCC[C@H](N)C(=O)O
|
| ZINC1742220 | 0.516 | 201.3 Da LogP 2.54 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCC[C@H](N)C(=O)O
|
| ZINC2035155 | 0.516 | 215.3 Da LogP 2.93 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCC[C@@H](N)C(=O)O
|
| ZINC2035157 | 0.516 | 201.3 Da LogP 2.54 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCC[C@@H](N)C(=O)O
|
| ZINC2037129 | 0.516 | 243.4 Da LogP 3.71 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCC[C@@H](N)C(=O)O
|
| ZINC43531622 | 0.516 | 271.4 Da LogP 4.49 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCC[C@H](N)C(=O)O
|
| ZINC43531626 | 0.516 | 271.4 Da LogP 4.49 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCC[C@@H](N)C(=O)O
|
| ZINC8437446 | 0.516 | 229.4 Da LogP 3.32 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCC[C@@H](N)C(=O)O
|
| ZINC2382564 | 0.514 | 217.3 Da LogP 0.91 TPSA 89.6 | ✓ Ro5 | ✓ Clean |
CC(C)(C)OC(=O)CCC[C@H](N)C(=O)O
|
| ZINC71613550 | 0.514 | 217.3 Da LogP 0.91 TPSA 89.6 | ✓ Ro5 | ✓ Clean |
CC(C)(C)OC(=O)CCC[C@@H](N)C(=O)O
|
| ZINC1529331 | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@H](C(=O)O)[C@@H](O)C(=O)O
|
| ZINC1529332 | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@H](C(=O)O)[C@H](O)C(=O)O
|
| ZINC1529333 | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@@H](C(=O)O)[C@@H](O)C(=O)O
|
| ZINC1529334 | 0.500 | 206.1 Da LogP -2.21 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)C(=O)[C@@H](C(=O)O)[C@H](O)C(=O)O
|
| ZINC2140007 | 0.500 | 225.2 Da LogP 0.14 TPSA 120.9 | ✓ Ro5 | ✓ Clean |
C[C@@](N)(CCCCP(=O)(O)O)C(=O)O
|
| ZINC2140009 | 0.500 | 225.2 Da LogP 0.14 TPSA 120.9 | ✓ Ro5 | ✓ Clean |
C[C@](N)(CCCCP(=O)(O)O)C(=O)O
|
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.