Protein profile
KP13_03918
Putative isochorismatase family protein rutB
Genome: KpKP13
Overview
Basic information about this protein and its source genome.
- Accession
- KP13_03918
- Gene
- rutB AHE45336.1
- Status
- annotated
- Amino acids
- 236
- 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)
- Y
- DEG identity (%)
- 88.444
- DEG E-value
- 4.12e-152
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 95.55
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.
Enzyme Commission (EC)
1Gene Ontology (GO)
3- GO:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
- GO:0019740 A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary nitrogen source, usually ammonia, and then activates genes to scavenge the last traces of the primary nitrogen source and to transport and metabolize alternative nitrogen sources. The utilization process begins when the cell or organism detects nitrogen levels, includes the activation of genes whose products detect, transport or metabolize nitrogen-containing substances, and ends when nitrogen is incorporated into the cell or organism's metabolism.
- GO:0006212 The chemical reactions and pathways resulting in the breakdown of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 18 | 215 | Pfam | PF00857 | Isochorismatase family |
| 18 | 215 | InterPro | IPR000868 | Isochorismatase-like |
| 3 | 221 | SUPERFAMILY | SSF52499 | Isochorismatase-like hydrolases |
| 3 | 221 | InterPro | IPR036380 | Isochorismatase-like superfamily |
| 19 | 205 | CDD | cd00431 | cysteine_hydrolases |
| 3 | 225 | NCBIfam | TIGR03614 | pyrimidine utilization protein B |
| 3 | 225 | InterPro | IPR019916 | Ureidoacrylate amidohydrolase RutB |
| 1 | 228 | Hamap | MF_00830 | Ureidoacrylate amidohydrolase RutB [rutB]. |
| 1 | 228 | InterPro | IPR019916 | Ureidoacrylate amidohydrolase RutB |
| 11 | 224 | PANTHER | PTHR43540 | PEROXYUREIDOACRYLATE/UREIDOACRYLATE AMIDOHYDROLASE-RELATED |
| 7 | 234 | Gene3D | G3DSA:3.40.50.850 | - |
| 7 | 234 | InterPro | IPR036380 | Isochorismatase-like superfamily |
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_A0A0H3GR97
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_03918
|
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 | 0.608 | ||||||
| 3 | 0.536 |
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 | 10.34 | 0.555 | ||||||
| 2 | 1.9 | 0.038 | ||||||
| 3 | 1.57 | 0.024 | ||||||
| 4 | 0.94 | 0.004 |
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 |
|---|---|---|---|---|---|---|---|
| 2 | 0.577 |
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 | 10.0 | 0.538 | ||||||
| 2 | 1.89 | 0.038 |
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 |
|---|---|---|---|---|---|---|
| BTB | Q1M7F4 | 209.2 Da LogP -3.01 TPSA 104.4 | ✓ Ro5 | ✓ Clean |
C(CO)N(CCO)C(CO)(CO)CO
|
|
| C5J | H8ZKV9 | 103.1 Da LogP -1.27 TPSA 98.2 | ✓ Ro5 | ✓ Clean |
C(=O)(N)NC(=O)N
|
|
| ISC | P0C6D3 | 226.2 Da LogP -0.09 TPSA 104.1 | ✓ Ro5 | ✓ Clean |
C=C(C(=O)O)O[C@H]1C=CC=C([C@@H]1O)C(=O)O
|
|
| NH4 | A6TWT6 | 18.0 Da LogP 0.38 TPSA 36.5 | ✓ Ro5 | ✓ Clean |
[NH4+]
|
|
| QLI | Q51790 | 225.2 Da LogP -0.12 TPSA 109.9 | ✓ Ro5 | ✓ Clean |
C=C(C(=O)O)O[C@H]1C=CC=C([C@@H]1N)C(=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
|
| 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
|
| ZINC1664923 | 0.500 | 234.2 Da LogP -1.40 TPSA 162.8 | ✓ Ro5 | ✓ Clean |
NC(=O)NC(=O)OCCOC(=O)NC(N)=O
|
| ZINC4722892 | 0.500 | 205.4 Da LogP 0.55 TPSA 72.2 | ✓ Ro5 | ✓ Clean |
NC(=O)NC(=O)C(Cl)(Cl)Cl
|
| 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.