Protein target profile
VK055_0055
alpha,alpha-trehalose-phosphate synthase
Strong target candidate with converging metabolic, structural and chemical evidence.
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
- 1.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 34.304 Higher values support similarity to known essential genes.
Localization
- Localization
- Unknown
Structure confidence
- ColabFold pLDDT
- 93.25 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
Pathways
Sequence
Primary amino-acid sequence viewer.
MSRLVVVSNRIALPDDKKSSAGGLAVGILGALRAAGGLWFGWSGEIGDDQQPLKQVSRGNISWASFNLNERDHDEYYNQFSNAVLWPAFHYRLDLVSFQREAWEGYLRVNAMLADKLLPLIEPDDTLWIHDYHLLPFASELRKRGVNNRIGFFLHIPFPTPEIFNALPPHAELLEQLCDYDLLGFQTESDRTAFLDSIAMQTRLSDLGDKRYQAWGKAFSTEVYPIGIDPDEITRNAKGPLPPKLAQLKNELKNVKNIFSVERLDYSKGLPERFLAYETLLEKYPQHHGKIRYTQIAPTSRGDVQAYQDIRHQLETAAGRINGQFGQLGWTPLYYLNQHFDRKLLMKVFRYSDVGLVTPLRDGMNLVAKEYVAAQDPDNPGVLVLSQFAGAAQELTSALIVNPYDRDEVAAALDRALSMLLAERIARHSAMLDVIRENDIHNWQARFVEDLQHISPRSEESRLRGKIATFPKLA
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
3- GO:0005992 The chemical reactions and pathways resulting in the formation of trehalose, a disaccharide that consists of two molecules of glucose and is isomeric with sucrose.
- GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
- GO:0003825 Catalysis of the reaction: UDP-glucose + D-glucose-6-phosphate = UDP + alpha,alpha-trehalose-6-phosphate.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 3 | 452 | NCBIfam | TIGR02400 | alpha,alpha-trehalose-phosphate synthase (UDP-forming) |
| 3 | 452 | InterPro | IPR012766 | Alpha,alpha-trehalose-phosphate synthase |
| 21 | 42 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 1 | 20 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. |
| 3 | 460 | PANTHER | PTHR10788 | TREHALOSE-6-PHOSPHATE SYNTHASE |
| 3 | 460 | InterPro | IPR001830 | Glycosyl transferase, family 20 |
| 230 | 437 | FunFam | G3DSA:3.40.50.2000:FF:000024 | Trehalose-6-phosphate synthase |
| 2 | 454 | SUPERFAMILY | SSF53756 | UDP-Glycosyltransferase/glycogen phosphorylase |
| 3 | 452 | CDD | cd03788 | GT20_TPS |
| 3 | 452 | InterPro | IPR001830 | Glycosyl transferase, family 20 |
| 20 | 449 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; |
| 21 | 43 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 43 | 474 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 230 | 437 | Gene3D | G3DSA:3.40.50.2000 | Glycogen Phosphorylase B; |
| 17 | 452 | Pfam | PF00982 | Glycosyltransferase family 20 |
| 17 | 452 | InterPro | IPR001830 | Glycosyl transferase, family 20 |
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
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 + 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_A0A0H3GVI4
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_0055
|
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 |
|---|---|---|---|---|---|---|
| ADQ RCSB PDB | G7CGT2 | 589.3 Da LogP -3.92 TPSA 311.7 | 3 viol. | ✓ Clean |
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
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|
| GDG RCSB PDB | G7CGT2 | 605.3 Da LogP -4.63 TPSA 331.7 | 3 viol. | ✓ Clean |
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
|
|
| NHE RCSB PDB | G7CGT2 | 207.3 Da LogP 0.80 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
C1CCC(CC1)NCCS(=O)(=O)O
|
|
| U2F RCSB PDB | P31677 | 568.3 Da LogP -3.82 TPSA 276.8 | 3 viol. | ✓ Clean |
C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
|
|
| UPG RCSB PDB | Q92410 | 566.3 Da LogP -4.79 TPSA 297.0 | 3 viol. | ✓ Clean |
C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
|
|
| VDM RCSB PDB | Q4WHW0 | 335.4 Da LogP -4.58 TPSA 173.9 | 1 viol. | ✓ Clean |
C1[C@@H]([C@H]([C@@H]([C@H]([C@H]1N[C@H]2C=C([C…
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|
| VDO RCSB PDB | P31677 | 415.3 Da LogP -4.46 TPSA 220.4 | 1 viol. | ✓ Clean |
C1[C@@H]([C@H]([C@@H]([C@H]([C@H]1N[C@H]2C=C([C…
|
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 |
|---|---|---|---|---|---|
| ZINC1710230 ZINC | 1.000 | 207.3 Da LogP 0.80 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCNC1CCCCC1
|
| ZINC2004372 ZINC | 0.786 | 221.3 Da LogP 1.19 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCCNC1CCCCC1
|
| ZINC38364153 ZINC | 0.786 | 235.3 Da LogP 1.58 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCCCNC1CCCCC1
|
| ZINC12959005 ZINC | 0.705 | 484.1 Da LogP -2.50 TPSA 264.4 | 2 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)…
|
| ZINC12959016 ZINC | 0.705 | 484.1 Da LogP -2.50 TPSA 264.4 | 2 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O…
|
| ZINC13548378 ZINC | 0.705 | 484.1 Da LogP -2.50 TPSA 264.4 | 2 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…
|
| ZINC25726233 ZINC | 0.705 | 484.1 Da LogP -2.50 TPSA 264.4 | 2 viol. | ✓ Clean |
O=c1ccn([C@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O)…
|
| ZINC3861755 ZINC | 0.705 | 484.1 Da LogP -2.50 TPSA 264.4 | 2 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…
|
| ZINC3875255 ZINC | 0.705 | 484.1 Da LogP -2.50 TPSA 264.4 | 2 viol. | ✓ Clean |
O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…
|
| ZINC3875256 ZINC | 0.705 | 484.1 Da LogP -2.50 TPSA 264.4 | 2 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)…
|
| ZINC3875257 ZINC | 0.705 | 484.1 Da LogP -2.50 TPSA 264.4 | 2 viol. | ✓ Clean |
O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…
|
| ZINC3875258 ZINC | 0.705 | 484.1 Da LogP -2.50 TPSA 264.4 | 2 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)…
|
| ZINC88466482 ZINC | 0.705 | 484.1 Da LogP -2.50 TPSA 264.4 | 2 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…
|
| ZINC35636069 ZINC | 0.700 | 404.2 Da LogP -2.62 TPSA 217.8 | 1 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)OP(=O)(O)O)[…
|
| ZINC40655887 ZINC | 0.700 | 404.2 Da LogP -2.62 TPSA 217.8 | 1 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)OP(=O)(O)O)[…
|
| ZINC40655889 ZINC | 0.700 | 404.2 Da LogP -2.62 TPSA 217.8 | 1 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)…
|
| ZINC44460318 ZINC | 0.700 | 404.2 Da LogP -2.62 TPSA 217.8 | 1 viol. | ✓ Clean |
O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…
|
| ZINC4490939 ZINC | 0.700 | 404.2 Da LogP -2.62 TPSA 217.8 | 1 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)…
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| ZINC8585026 ZINC | 0.700 | 404.2 Da LogP -2.62 TPSA 217.8 | 1 viol. | ✓ Clean |
O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…
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| ZINC8585028 ZINC | 0.700 | 404.2 Da LogP -2.62 TPSA 217.8 | 1 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O…
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| ZINC8585030 ZINC | 0.700 | 404.2 Da LogP -2.62 TPSA 217.8 | 1 viol. | ✓ Clean |
O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…
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| ZINC8585032 ZINC | 0.700 | 404.2 Da LogP -2.62 TPSA 217.8 | 1 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O…
|
| ZINC108477652 ZINC | 0.688 | 486.1 Da LogP -1.52 TPSA 244.1 | 2 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)…
|
| ZINC220143873 ZINC | 0.688 | 486.1 Da LogP -1.52 TPSA 244.1 | 2 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…
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| ZINC31519946 ZINC | 0.688 | 486.1 Da LogP -1.52 TPSA 244.1 | 2 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)…
|
| ZINC90614026 ZINC | 0.688 | 486.1 Da LogP -1.52 TPSA 244.1 | 2 viol. | ✓ Clean |
O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…
|
| ZINC16052241 ZINC | 0.681 | 335.4 Da LogP -4.58 TPSA 173.9 | 1 viol. | ✓ Clean |
OCC1=C[C@H](N[C@H]2C[C@H](CO)[C@@H](O)[C@H](O)[…
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| ZINC4188096 ZINC | 0.661 | 297.3 Da LogP -2.62 TPSA 159.8 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…
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| ZINC4188103 ZINC | 0.661 | 297.3 Da LogP -2.62 TPSA 159.8 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…
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| ZINC4188112 ZINC | 0.661 | 297.3 Da LogP -2.62 TPSA 159.8 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…
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| ZINC4188116 ZINC | 0.661 | 297.3 Da LogP -2.62 TPSA 159.8 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…
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| ZINC102211562 ZINC | 0.652 | 490.3 Da LogP -1.89 TPSA 206.8 | 1 viol. | ✓ Clean |
C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…
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| ZINC110347779 ZINC | 0.652 | 490.3 Da LogP -1.89 TPSA 206.8 | 1 viol. | ✓ Clean |
C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…
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| ZINC110347782 ZINC | 0.652 | 490.3 Da LogP -1.89 TPSA 206.8 | 1 viol. | ✓ Clean |
C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…
|
| ZINC97976147 ZINC | 0.652 | 490.3 Da LogP -1.89 TPSA 206.8 | 1 viol. | ✓ Clean |
C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…
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| ZINC2047403 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1O
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| ZINC2047673 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1O
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| ZINC2169830 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
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| ZINC3201876 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O
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| ZINC3201878 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…
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| ZINC3830178 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1O
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| ZINC3830179 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1O
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| ZINC3978047 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@H]1O
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| ZINC3978048 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@H](O)[C@H]1O
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| ZINC3978049 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1O
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| ZINC4048240 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O
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| ZINC8580514 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O
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| ZINC895113 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O
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| ZINC896706 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O
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| ZINC970363 ZINC | 0.644 | 267.2 Da LogP -1.98 TPSA 139.5 | ✓ Ro5 | ✓ Clean |
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O
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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.