Natural Product: NPC282812

Natural Product IDNPC282812
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 AEMOLEFTQBMNLQ-FOSXNRGSSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 90062900
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0000215] Sugar acids and derivatives
            • [CHEMONTID:0002094] Glucuronic acid derivatives

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey AEMOLEFTQBMNLQ-FOSXNRGSSA-N
Standard InCHI InChI=1S/C6H10O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,6-9,12H,(H,10,11)/t1-,2+,3-,4+,6-/m0/s1
SMILES [C@@H]1([C@H]([C@H](C(=O)O)O[C@@H]([C@H]1O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   194.04 Volume:   162.671
?
Van der Waals volume.
Dense:   1.193 LogP:   -1.538
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.817
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   0.446
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   7.0
TPSA:   127.45
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   5.0 Rings:   1.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.298 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.702 Fsp3:   0.833
MCE-18:   26.182
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.054 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.056
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.506 Promiscuous compounds:   0.2

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.284 MDCK Permeability:   -4.844
Pgp-inhibitor:   0.0 Pgp-substrate:   0.674
PAMPA:   1.0
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.185
20% Bioavailability (F20%):   0.024 30% Bioavailability (F30%):   0.019
50% Bioavailability (F50%):   0.299

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.764
Plasma Protein Binding (PPB):   28.027% Volume Distribution (VD):   -0.637
Fu: 82.185%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.07
OATP1B3 inhibitor:   0.15 BCRP inhibitor:   0.014
BSEP inhibitor:   0.006

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.077 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.626
HLM stability:   0.003
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  1.453 Half-life (T1/2):  2.629

ADMET: Toxicity

hERG Blockers:  0.013 hERG Blockers (10um):  0.095
Human Hepatotoxicity (H-HT):  0.326 Drug-induced Liver Injury (DILI):  0.202
AMES Toxicity:  0.484 Rat Oral Acute Toxicity:  0.06
Maximum Recommended Daily Dose:  0.024 Skin Sensitization:  0.771
Carcinogencity:  0.098 Eye Corrosion:  0.072
Eye Irritation:  0.893 Respiratory Toxicity:  0.053
Drug-induced Neurotoxicity:  0.016 Ototoxicity:  0.809
Hematotoxicity:  0.253 Drug-induced Nephrotoxicity:  0.482
Genotoxicity:  0.078 RPMI-8226 Immunitoxicity:  0.033
A549 Cytotoxicity:  0.009 Hek293 Cytotoxicity:  0.016
BCF:   0.132
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   2.159
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.568
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.918
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)00169-2]
NPO4654 Critonia quadrangularis Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)81431-4]
NPO25903 Swinglea glutinosa Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[11575960]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[11975485]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. fruit n.a. PMID[15128023]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[18068204]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[21446699]
NPO16601 Styrax perkinsiae Species Styracaceae Eukaryota n.a. bark n.a. PMID[26762060]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[31763840]
NPO12697 Baccharis megapotamica Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[3437280]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[9748368]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16522 Ceratozamia fuscoviridis Species Zamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO24501 Asteriscus graveolens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26436 Citrus glauca Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15024 Senecio rivularis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15531 Quercus dentata Species Fagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13719 Salacia prinoides Species Sertulariidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14892 Flemingia congesta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9196 Aconitum sachalinense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10247 Orthosphenia mexicana Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12697 Baccharis megapotamica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14046 Stevia mercedensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16766 Haplophyllum dauricum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16856 Solanum elaeagnifolium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21913 Verbesina rupestris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15760 Aconitum pseudohuiliense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17259 Thuja standishii Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11233 Pseudocyphellaria impressa Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13563 Alstonia deplanchei Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25903 Swinglea glutinosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12438 Fomes cajanderi Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11915 Lecanora planaica Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Petiole n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13719 Salacia prinoides Species Sertulariidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15024 Senecio rivularis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17259 Thuja standishii Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9196 Aconitum sachalinense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13719 Salacia prinoides Species Sertulariidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10247 Orthosphenia mexicana Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17259 Thuja standishii Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16289 Marrubium supinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15760 Aconitum pseudohuiliense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9196 Aconitum sachalinense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15024 Senecio rivularis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9196 Aconitum sachalinense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14892 Flemingia congesta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4448 Relhania pumila Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16435 Cacalia bicolor Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24501 Asteriscus graveolens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26436 Citrus glauca Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15969 Alcyonium molle Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17259 Thuja standishii Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4654 Critonia quadrangularis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21913 Verbesina rupestris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13396 Aplophyllum popovii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO2372 Cryptotermes cynocephalus Species Termitoidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16289 Marrubium supinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18873.8 Salmonella enterica subsp. enterica serovar typhimurium Subspecies Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12438 Fomes cajanderi Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29175 Strychnos tabascana Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9196 Aconitum sachalinense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14046 Stevia mercedensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11915 Lecanora planaica Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16856 Solanum elaeagnifolium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9107 Metalasia bolusii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO576 Oxyanthus speciosus Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15024 Senecio rivularis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14572 Senecio latifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5468 Dacrydium fonki Species Mytilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13719 Salacia prinoides Species Sertulariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16071 Erigeron crispus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14413 Bombus muscorum Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15531 Quercus dentata Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7515 Codium decorticatum Species Codiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13872 Amanita cokeri Species Amanitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9823 Centrosema pascuorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13563 Alstonia deplanchei Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10247 Orthosphenia mexicana Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25903 Swinglea glutinosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16522 Ceratozamia fuscoviridis Species Zamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16766 Haplophyllum dauricum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14723 Streptomyces xantholiticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10802 Rhinoceros sondaicus Species Rhinocerotidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11233 Pseudocyphellaria impressa Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16601 Styrax perkinsiae Species Styracaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12697 Baccharis megapotamica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15760 Aconitum pseudohuiliense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC282812 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC317651
1.0 High Similarity NPC258690

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC282812 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.5625 Remote Similarity NPD8961 Phase 4

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data