Protein target profile
VK055_2907
ribosome small subunit-dependent GTPase A
Promising target candidate with multiple supporting evidence streams.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Risks to review
Evidence coverage
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
- No hit
- Gut microbiome similarity
- 3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- Y
- DEG identity (%)
- 88.952 Higher values support similarity to known essential genes.
- DEG E-value
- 0.0 Smaller values mean stronger essential-gene similarity.
Localization
- Localization
- Cytoplasmic
Structure confidence
- ColabFold pLDDT
- 79.2 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelThe 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.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.
Sequence
Sequence
Primary amino-acid sequence viewer.
MSKNKLSKGQQRRVKANHQRRLKTTAEKADYDDNLFGETSEGIVISRFGMHADVESADGSVHRCNIRRTIRSLVTGDRVVWRPGKDAADGVSVKGIVEAVHDRASVLTRPDFYDGVKPIAANIDQIVVVSAILPELSLNIIDRYLVACEAQDIEPLIVLNKIDLLDDDGLRFVNEQMDIYRNIGYRVLLVSSRTQDGLKPLEAALTDRISIFAGQSGVGKSSLLNALLGLNEDQILTNDVSDVSGLGQHTTTAARLYHFPHGGDVIDSPGVREFGLWHLEAEQITNGFVEFHDYLGRCKYRDCKHDTDPGCALREAVENGKIAESRFENYHRILESMAQVQVKTRKNFSSSDD
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
6- GO:0005525 Binding to GTP, guanosine triphosphate.
- GO:0003924 Catalysis of the reaction: GTP + H2O = GDP + H+ + phosphate.
- GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
- GO:0046872 Binding to a metal ion.
- GO:0019843 Binding to a ribosomal RNA.
- GO:0042274 A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 35 | 102 | Gene3D | G3DSA:2.40.50.140 | - |
| 35 | 102 | InterPro | IPR012340 | Nucleic acid-binding, OB-fold |
| 103 | 276 | Gene3D | G3DSA:3.40.50.300 | - |
| 103 | 276 | InterPro | IPR027417 | P-loop containing nucleoside triphosphate hydrolase |
| 121 | 335 | CDD | cd01854 | YjeQ_EngC |
| 121 | 335 | InterPro | IPR004881 | Ribosome biogenesis GTPase RsgA |
| 73 | 335 | NCBIfam | TIGR00157 | ribosome small subunit-dependent GTPase A |
| 73 | 335 | InterPro | IPR004881 | Ribosome biogenesis GTPase RsgA |
| 277 | 353 | Gene3D | G3DSA:1.10.40.50 | Probable gtpase engc; domain 3 |
| 104 | 274 | ProSiteProfiles | PS51721 | Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. |
| 104 | 274 | InterPro | IPR030378 | Circularly permuted (CP)-type guanine nucleotide-binding (G) domain |
| 40 | 341 | Hamap | MF_01820 | Small ribosomal subunit biogenesis GTPase RsgA [rsgA]. |
| 40 | 341 | InterPro | IPR004881 | Ribosome biogenesis GTPase RsgA |
| 121 | 272 | ProSiteProfiles | PS50936 | EngC GTPase domain profile. |
| 121 | 272 | InterPro | IPR010914 | RsgA GTPase domain |
| 103 | 276 | FunFam | G3DSA:3.40.50.300:FF:000389 | Small ribosomal subunit biogenesis GTPase RsgA |
| 114 | 340 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases |
| 114 | 340 | InterPro | IPR027417 | P-loop containing nucleoside triphosphate hydrolase |
| 100 | 277 | Pfam | PF03193 | RsgA GTPase |
| 100 | 277 | InterPro | IPR010914 | RsgA GTPase domain |
| 20 | 347 | PANTHER | PTHR32120 | SMALL RIBOSOMAL SUBUNIT BIOGENESIS GTPASE RSGA |
| 20 | 347 | InterPro | IPR004881 | Ribosome biogenesis GTPase RsgA |
| 1 | 24 | MobiDBLite | mobidb-lite | consensus disorder prediction |
| 1 | 19 | MobiDBLite | mobidb-lite | consensus disorder prediction |
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
Residue sets
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
Residue sets
All structural evidence
Structural evidence
0 + 2Experimental 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
AF_A0A0H3GI06
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_2907
|
ColabFold | — | — | full sequence | — | Loaded |
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| G4P RCSB PDB | Q9KX08 | 603.2 Da LogP -2.22 TPSA 345.6 | 3 viol. | ✓ Clean |
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
|
|
| GGM RCSB PDB | P39286 | 655.3 Da LogP -0.86 TPSA 320.0 | 3 viol. | ✓ Clean |
CNc1ccccc1C(=O)O[C@@H]2[C@H](O[C@H]([C@@H]2O)n3…
|
|
| GNP RCSB PDB | P39286 | 522.2 Da LogP -2.76 TPSA 301.9 | 3 viol. | ✓ Clean |
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
|
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| IUM RCSB PDB | O34530 | 270.0 Da LogP -2.38 TPSA 46.1 | ✓ Ro5 | ✓ Clean |
[O-][U+4][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 |
|---|---|---|---|---|---|
| ZINC104869865 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…
|
| ZINC12504289 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC34541308 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC35000839 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…
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| ZINC45284491 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC80639694 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC8215481 ZINC | 0.836 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC12503703 ZINC | 0.738 | 427.2 Da LogP -1.42 TPSA 232.3 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(…
|
| ZINC8215878 ZINC | 0.738 | 427.2 Da LogP -1.42 TPSA 232.3 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O…
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| ZINC12503440 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](OP(=O)(O)O)…
|
| ZINC1530370 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](OP(=O)(O)O)[…
|
| ZINC28631009 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](OP(=O)(O)O)[…
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| ZINC3872740 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…
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| ZINC3872741 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…
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| ZINC3872742 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…
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| ZINC3872743 ZINC | 0.719 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…
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| ZINC12501413 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…
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| ZINC12958448 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…
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| ZINC1532555 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…
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| ZINC16546189 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…
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| ZINC2159505 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…
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| ZINC3073318 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…
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| ZINC3869963 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…
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| ZINC3869965 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…
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| ZINC9334496 ZINC | 0.714 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…
|
| ZINC12501360 ZINC | 0.657 | 363.2 Da LogP -2.57 TPSA 206.0 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2OP…
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| ZINC100058967 ZINC | 0.632 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc(=O)c2ncn([C@H]3O[C@H](CO[P@](=O)(O)OP(=O)…
|
| ZINC12504287 ZINC | 0.632 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…
|
| ZINC12504288 ZINC | 0.632 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc(=O)c2ncn([C@H]3O[C@@H](CO[P@@](=O)(O)OP(=…
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| ZINC31308647 ZINC | 0.632 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…
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| ZINC106686432 ZINC | 0.627 | 428.2 Da LogP -2.03 TPSA 226.5 | 2 viol. | ✓ Clean |
O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP…
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| ZINC12296728 ZINC | 0.627 | 347.2 Da LogP -1.54 TPSA 185.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)…
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| ZINC12958393 ZINC | 0.627 | 428.2 Da LogP -2.03 TPSA 226.5 | 2 viol. | ✓ Clean |
O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)O…
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| ZINC13527599 ZINC | 0.627 | 347.2 Da LogP -1.54 TPSA 185.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O…
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| ZINC13527603 ZINC | 0.627 | 347.2 Da LogP -1.54 TPSA 185.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)…
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| ZINC1532627 ZINC | 0.627 | 347.2 Da LogP -1.54 TPSA 185.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)…
|
| ZINC1730395 ZINC | 0.627 | 347.2 Da LogP -1.54 TPSA 185.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O…
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| ZINC35024781 ZINC | 0.627 | 428.2 Da LogP -2.03 TPSA 226.5 | 2 viol. | ✓ Clean |
O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)O…
|
| ZINC35024785 ZINC | 0.627 | 428.2 Da LogP -2.03 TPSA 226.5 | 2 viol. | ✓ Clean |
O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)O…
|
| ZINC35024786 ZINC | 0.627 | 428.2 Da LogP -2.03 TPSA 226.5 | 2 viol. | ✓ Clean |
O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)…
|
| ZINC3869846 ZINC | 0.627 | 347.2 Da LogP -1.54 TPSA 185.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O…
|
| ZINC3869847 ZINC | 0.627 | 347.2 Da LogP -1.54 TPSA 185.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2…
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| ZINC3869848 ZINC | 0.627 | 347.2 Da LogP -1.54 TPSA 185.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O…
|
| ZINC4261903 ZINC | 0.627 | 428.2 Da LogP -2.03 TPSA 226.5 | 2 viol. | ✓ Clean |
O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)O…
|
| ZINC80601236 ZINC | 0.627 | 428.2 Da LogP -2.03 TPSA 226.5 | 2 viol. | ✓ Clean |
O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)O…
|
| ZINC95921560 ZINC | 0.627 | 428.2 Da LogP -2.03 TPSA 226.5 | 2 viol. | ✓ Clean |
O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)O…
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| ZINC71774763 ZINC | 0.625 | 432.3 Da LogP -2.23 TPSA 198.3 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@](=O)(O)N3CCOCC3…
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| ZINC100727895 ZINC | 0.621 | 347.2 Da LogP -2.50 TPSA 196.8 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2P(=…
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| ZINC17610743 ZINC | 0.621 | 347.2 Da LogP -2.50 TPSA 196.8 | 1 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2P(…
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| ZINC32023359 ZINC | 0.614 | 487.2 Da LogP 0.16 TPSA 249.4 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2C=C[C@H](CO[P@](=O)(O)O[P@](…
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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.