Protein target profile
HT085_RS00185
tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB
Target candidate with partial support; inspect missing evidence before prioritizing.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Terms and data sources used on this page
PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.
AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.
ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.
pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.
FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.
Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.
PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.
ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.
ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.
LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.
Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.
DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.
Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.
EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.
KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.
Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.
Prioritization evidence
Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.
Off-target risk
- Human off-target
- Hit
- Gut microbiome off-target
- Hit
Essentiality
- Essential (DEG)
- N
Localization
- Localization
- Cytoplasmic
Binding-site evidence
The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.
Sequence
Primary amino-acid sequence viewer.
MKKVFIRTFGCQMNEYDSEKMLSVLAEEHGGIEQVTQADEADIILFNTCSVREKAQEKVFSDLGRVRPLKEKNPGLIIGVAGCVASQEGENIIKRAPYVDVVFGPQTLHRLPKMIVDKETSGLSQVDISFPEIEKFDHLPPARVEGGAAFVSIMEGCSKYCSFCVVPYTRGEEFSRPLNDVLTEIANLAQQGVKEINLLGQNVNAYRGEMDDGEICDFATLLRIVHEIPGIERMRFTTSHPREFTDSIIECYRDLPKLVSHLHLPIQSGSDRVLSAMKRGYTALEYKSIIRKLRAIRPDLCLSSDFIVGFPGETEREFEQTLKLVKDIAFDLSFVFIYSPRPGTPAANLPDDTPHEEKVRRLEALNEVIEAETARINQTMIGTVQRCLVEGISKKDPDQLQARTANNRVVNFTGTPDMINQMIDLEITEAYTFSLRGKIVEA
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
4- GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
- GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
- GO:0046872 Binding to a metal ion.
- GO:0035597 Catalysis of the reaction: N(6)-dimethylallyladenosine(37) in tRNA + [sulfur carrier]-SH + AH2 + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + [sulfur carrier]-H + 5'-deoxyadenosine + L-methionine + A + S-adenosyl-L-homocysteine + 2 H+.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 3 | 440 | NCBIfam | TIGR01574 | tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB |
| 2 | 130 | FunFam | G3DSA:3.40.50.12160:FF:000001 | tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase |
| 1 | 441 | SFLD | SFLDF00273 | (dimethylallyl)adenosine tRNA methylthiotransferase (MiaB-like) |
| 1 | 441 | InterPro | IPR006463 | tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB |
| 378 | 440 | Pfam | PF01938 | TRAM domain |
| 378 | 440 | InterPro | IPR002792 | TRAM domain |
| 378 | 441 | ProSiteProfiles | PS50926 | TRAM domain profile. |
| 378 | 441 | InterPro | IPR002792 | TRAM domain |
| 2 | 131 | Gene3D | G3DSA:3.40.50.12160 | - |
| 2 | 131 | InterPro | IPR038135 | Methylthiotransferase, N-terminal domain superfamily |
| 145 | 381 | FunFam | G3DSA:3.80.30.20:FF:000001 | tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase 2 |
| 37 | 354 | SFLD | SFLDG01082 | B12-binding domain containing |
| 143 | 375 | ProSiteProfiles | PS51918 | Radical SAM core domain profile. |
| 143 | 375 | InterPro | IPR007197 | Radical SAM |
| 1 | 441 | SFLD | SFLDG01061 | methylthiotransferase |
| 1 | 441 | InterPro | IPR005839 | Methylthiotransferase |
| 151 | 171 | ProSitePatterns | PS01278 | Methylthiotransferase radical SAM domain signature. |
| 151 | 171 | InterPro | IPR020612 | Methylthiotransferase, conserved site |
| 355 | 375 | Coils | Coil | Coil |
| 145 | 380 | Gene3D | G3DSA:3.80.30.20 | tm_1862 like domain |
| 145 | 380 | InterPro | IPR023404 | Radical SAM, alpha/beta horseshoe |
| 156 | 364 | CDD | cd01335 | Radical_SAM |
| 129 | 371 | SUPERFAMILY | SSF102114 | Radical SAM enzymes |
| 2 | 120 | ProSiteProfiles | PS51449 | Methylthiotransferase N-terminal domain profile. |
| 2 | 120 | InterPro | IPR013848 | Methylthiotransferase, N-terminal |
| 2 | 441 | Hamap | MF_01864 | tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase [miaB]. |
| 2 | 441 | InterPro | IPR006463 | tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB |
| 151 | 325 | Pfam | PF04055 | Radical SAM superfamily |
| 151 | 325 | InterPro | IPR007197 | Radical SAM |
| 3 | 437 | NCBIfam | TIGR00089 | MiaB/RimO family radical SAM methylthiotransferase |
| 3 | 437 | InterPro | IPR005839 | Methylthiotransferase |
| 147 | 364 | SMART | SM00729 | MiaB |
| 147 | 364 | InterPro | IPR006638 | Elp3/MiaA/NifB-like, radical SAM core domain |
| 3 | 104 | Pfam | PF00919 | Uncharacterized protein family UPF0004 |
| 3 | 104 | InterPro | IPR013848 | Methylthiotransferase, N-terminal |
| 2 | 441 | PANTHER | PTHR43020 | CDK5 REGULATORY SUBUNIT-ASSOCIATED PROTEIN 1 |
3D structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
All structural evidence
Structural evidence
0 + 1Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold DB
HT085_RS00185
|
AlphaFold DB | — | — | full sequence | — | Viewing |
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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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 |
|---|---|---|---|---|---|
| ZINC2004372 ZINC | 1.000 | 221.3 Da LogP 1.19 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCCNC1CCCCC1
|
| ZINC38364153 ZINC | 0.926 | 235.3 Da LogP 1.58 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCCCNC1CCCCC1
|
| ZINC1710230 ZINC | 0.786 | 207.3 Da LogP 0.80 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCNC1CCCCC1
|
| ZINC5188799 ZINC | 0.630 | 280.5 Da LogP 4.39 TPSA 24.1 | ✓ Ro5 | ✓ Clean |
C(CCCNC1CCCCC1)CCNC1CCCCC1
|
| ZINC2509149 ZINC | 0.531 | 211.4 Da LogP 4.27 TPSA 12.0 | ✓ Ro5 | ✓ Clean |
CCCCCCCCNC1CCCCC1
|
| ZINC130127586 ZINC | 0.529 | 260.4 Da LogP 1.38 TPSA 58.2 | ✓ Ro5 | ✓ Clean |
O=S(=O)(NCCNC1CCCCCC1)C1CC1
|
| ZINC19367005 ZINC | 0.519 | 224.4 Da LogP 2.83 TPSA 24.1 | ✓ Ro5 | ✓ Clean |
C1CCC(NCCNC2CCCCC2)CC1
|
| ZINC1672446 ZINC | 0.500 | 228.3 Da LogP 1.49 TPSA 75.3 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCCCNC1CCCCC1)C(=O)O
|
| ZINC2168583 ZINC | 0.500 | 237.3 Da LogP 0.16 TPSA 86.6 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)C[C@@H](O)CNC1CCCCC1
|
| ZINC2168584 ZINC | 0.500 | 237.3 Da LogP 0.16 TPSA 86.6 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)C[C@H](O)CNC1CCCCC1
|
| ZINC236994621 ZINC | 0.500 | 290.4 Da LogP 0.85 TPSA 75.3 | ✓ Ro5 | ✓ Clean |
CCS(=O)(=O)CC(=O)NCCNC1CCCCCC1
|
| ZINC44655186 ZINC | 0.500 | 213.4 Da LogP 3.12 TPSA 21.3 | ✓ Ro5 | ✓ Clean |
COCCCCNC1CCCCCCC1
|
| ZINC5840523 ZINC | 0.500 | 228.3 Da LogP 1.49 TPSA 75.3 | ✓ Ro5 | ✓ Clean |
N[C@H](CCCCNC1CCCCC1)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.