Protein profile
VK055_2645
putative D-serine deaminase (D-serine dehydratase) protein
Genome: KpATCC43816
Overview
Basic information about this protein and its source genome.
- Accession
- VK055_2645
- Gene
- AIK81239.1
- Status
- annotated
- Amino acids
- 391
- Structure source
- AlphaFold + ColabFold
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
- Cytoplasmic
- ColabFold pLDDT
- 93.07
Selected Druggability evidence
AlphaFold / UniProt modelSelected 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)
1- GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 12 | 389 | CDD | cd06818 | PLPDE_III_cryptic_DSD |
| 280 | 377 | Pfam | PF14031 | Putative serine dehydratase domain |
| 280 | 377 | InterPro | IPR026956 | D-serine dehydratase-like domain |
| 257 | 391 | Gene3D | G3DSA:2.40.37.20 | - |
| 257 | 391 | InterPro | IPR042208 | D-serine dehydratase-like domain superfamily |
| 22 | 254 | Gene3D | G3DSA:3.20.20.10 | Alanine racemase |
| 22 | 254 | InterPro | IPR029066 | PLP-binding barrel |
| 21 | 201 | Pfam | PF01168 | Alanine racemase, N-terminal domain |
| 21 | 201 | InterPro | IPR001608 | Alanine racemase, N-terminal |
| 6 | 383 | PANTHER | PTHR28004 | ZGC:162816-RELATED |
| 280 | 378 | SMART | SM01119 | D_ser_dehydrat_2 |
| 280 | 378 | InterPro | IPR026956 | D-serine dehydratase-like domain |
| 21 | 257 | SUPERFAMILY | SSF51419 | PLP-binding barrel |
| 21 | 257 | InterPro | IPR029066 | PLP-binding barrel |
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 + 2Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
AF_A0A0H3GR84
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_2645
|
ColabFold | — | — | full sequence | — | Loaded |
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer
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 | 8.49 | 0.453 |
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 | 8.38 | 0.447 |
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.
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 |
|---|---|---|---|---|---|
| ZINC2568071 | 0.519 | 218.3 Da LogP -1.08 TPSA 112.7 | ✓ Ro5 | ✓ Clean |
CC(C)[C@H](NC(=O)[C@@H](N)[C@@H](C)O)C(=O)O
|
| ZINC12359024 | 0.500 | 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 | 0.500 | 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 | 0.500 | 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 | 0.500 | 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 | 0.500 | 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
|
| ZINC2561115 | 0.500 | 321.3 Da LogP -3.49 TPSA 182.2 | 1 viol. | ✓ Clean |
C[C@@H](O)[C@H](N)C(=O)N[C@H](C(=O)N[C@H](C(=O)…
|
| ZINC3581021 | 0.500 | 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 | 0.500 | 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
|
| ZINC5462352 | 0.500 | 321.3 Da LogP -3.49 TPSA 182.2 | 1 viol. | ✓ Clean |
C[C@H](O)[C@H](N)C(=O)N[C@H](C(=O)N[C@H](C(=O)O…
|
| ZINC5462358 | 0.500 | 321.3 Da LogP -3.49 TPSA 182.2 | 1 viol. | ✓ Clean |
C[C@H](O)[C@@H](N)C(=O)N[C@H](C(=O)N[C@H](C(=O)…
|
| ZINC5462362 | 0.500 | 321.3 Da LogP -3.49 TPSA 182.2 | 1 viol. | ✓ Clean |
C[C@@H](O)[C@H](NC(=O)[C@@H](NC(=O)[C@H](N)[C@@…
|
| ZINC5783661 | 0.500 | 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 | 0.500 | 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
|
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.