Natural Product: NPC82905

Natural Product IDNPC82905
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 FYPLZVVQSPMLPL-DODNOZFWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003533] Flavonoid-7-O-glycosides

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 FYPLZVVQSPMLPL-DODNOZFWSA-N
Standard InCHI InChI=1S/C23H24O10/c1-29-12-5-3-11(4-6-12)15-9-14(25)19-16(30-2)7-13(8-17(19)32-15)31-23-22(28)21(27)20(26)18(10-24)33-23/h3-9,18,20-24,26-28H,10H2,1-2H3/t18-,20-,21+,22-,23-/m1/s1
SMILES COc1ccc(cc1)c1cc(=O)c2c(cc(cc2o1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   460.14 Volume:   438.949
?
Van der Waals volume.
Dense:   1.048 LogP:   1.435
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.858
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.682
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   24.0
TPSA:   148.05
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   4.0 Rings:   4.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.413 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.702 Fsp3:   0.348
MCE-18:   83.065
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.601 Fluc inhibitor:   0.445
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.947
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.808
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.092 Promiscuous compounds:   0.321

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.723 MDCK Permeability:   -4.995
Pgp-inhibitor:   0.012 Pgp-substrate:   0.286
PAMPA:   0.878
?
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):   0.857
20% Bioavailability (F20%):   0.242 30% Bioavailability (F30%):   0.927
50% Bioavailability (F50%):   0.961

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.393
Plasma Protein Binding (PPB):   87.986% Volume Distribution (VD):   -0.088
Fu: 13.321%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.849
BSEP inhibitor:   0.27

ADMET: Metabolism

CYP1A2-inhibitor:   0.055 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.003 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.029 CYP2D6-substrate:   0.024
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.01
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.998
HLM stability:   0.038
?
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):  3.216 Half-life (T1/2):  3.106

ADMET: Toxicity

hERG Blockers:  0.049 hERG Blockers (10um):  0.11
Human Hepatotoxicity (H-HT):  0.632 Drug-induced Liver Injury (DILI):  0.985
AMES Toxicity:  0.921 Rat Oral Acute Toxicity:  0.032
Maximum Recommended Daily Dose:  0.071 Skin Sensitization:  0.958
Carcinogencity:  0.583 Eye Corrosion:  0.0
Eye Irritation:  0.291 Respiratory Toxicity:  0.038
Drug-induced Neurotoxicity:  0.02 Ototoxicity:  0.818
Hematotoxicity:  0.418 Drug-induced Nephrotoxicity:  0.686
Genotoxicity:  0.834 RPMI-8226 Immunitoxicity:  0.112
A549 Cytotoxicity:  0.159 Hek293 Cytotoxicity:  0.339
BCF:   0.386
?
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:   3.192
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.586
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.827
?
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
NPO12373 Vinca minor Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[ 29131648]
NPO2471 Axinyssa variabilis Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12373 Vinca minor Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15456 Sideritis soluta Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11625 Markhamia stipulata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13327 Phomopsis leptostromiformis Species Valsaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16108 Eupatorium mikanioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7135 Mollugo spergula Species Molluginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6413 Viguiera stenoloba Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10011 Myrsine capitellata Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12373 Vinca minor Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16108 Eupatorium mikanioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10011 Myrsine capitellata Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7135 Mollugo spergula Species Molluginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12373 Vinca minor Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6413 Viguiera stenoloba Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15042 Lepraria membranacea Species Stereocaulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16108 Eupatorium mikanioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11625 Markhamia stipulata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9162 Nicotiana affinis Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11342 Sideritis trojana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6413 Viguiera stenoloba Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12373 Vinca minor Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6864 Lactarius spinosulus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12241 Hypericum reflexum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5805 Chlorociboria aeruginascens Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2471 Axinyssa variabilis Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10011 Myrsine capitellata Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15456 Sideritis soluta Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7135 Mollugo spergula Species Molluginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12598 Osteospermum fruticosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO944 Senecio sandersonii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13327 Phomopsis leptostromiformis Species Valsaceae 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 NPC82905 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
0.8429 Intermediate Similarity NPC610763
0.8056 Intermediate Similarity NPC182045
0.7639 Intermediate Similarity NPC110349
0.7297 Intermediate Similarity NPC95090
0.7297 Intermediate Similarity NPC27408
0.7143 Intermediate Similarity NPC284960
0.7125 Intermediate Similarity NPC473657
0.6974 Remote Similarity NPC186807
0.6933 Remote Similarity NPC58053
0.6707 Remote Similarity NPC295613
0.6406 Remote Similarity NPC101294
0.6296 Remote Similarity NPC22832
0.6296 Remote Similarity NPC243930
0.6282 Remote Similarity NPC83283
0.6282 Remote Similarity NPC143851
0.622 Remote Similarity NPC607707
0.6207 Remote Similarity NPC475366
0.6207 Remote Similarity NPC475497
0.6203 Remote Similarity NPC168822
0.6173 Remote Similarity NPC479402
0.6163 Remote Similarity NPC473512
0.6076 Remote Similarity NPC39360
0.6076 Remote Similarity NPC29763
0.6076 Remote Similarity NPC210003
0.6049 Remote Similarity NPC222936
0.6 Remote Similarity NPC93337
0.6 Remote Similarity NPC189142
0.6 Remote Similarity NPC77660
0.5976 Remote Similarity NPC609451
0.5926 Remote Similarity NPC181712
0.5926 Remote Similarity NPC105025
0.5926 Remote Similarity NPC45638
0.5904 Remote Similarity NPC605067
0.5854 Remote Similarity NPC100720
0.5854 Remote Similarity NPC201292
0.5843 Remote Similarity NPC284277
0.5833 Remote Similarity NPC311830
0.5795 Remote Similarity NPC129827
0.575 Remote Similarity NPC45165
0.5679 Remote Similarity NPC261866
0.5679 Remote Similarity NPC45618
0.5647 Remote Similarity NPC88023
0.5647 Remote Similarity NPC479406
0.5647 Remote Similarity NPC309025
0.561 Remote Similarity NPC146792
0.5591 Remote Similarity NPC475382
0.5581 Remote Similarity NPC479407
0.5568 Remote Similarity NPC603300
0.5556 Remote Similarity NPC135345
0.5542 Remote Similarity NPC58716
0.5529 Remote Similarity NPC601144
0.5506 Remote Similarity NPC15358
0.5488 Remote Similarity NPC289667
0.5476 Remote Similarity NPC472459
0.5465 Remote Similarity NPC602805
0.5441 Remote Similarity NPC278556
0.5417 Remote Similarity NPC244875
0.5412 Remote Similarity NPC191306
0.5357 Remote Similarity NPC84362
0.5352 Remote Similarity NPC70853
0.5349 Remote Similarity NPC80188
0.5349 Remote Similarity NPC486578
0.5341 Remote Similarity NPC211594
0.5316 Remote Similarity NPC280975
0.5287 Remote Similarity NPC220169
0.5275 Remote Similarity NPC22062
0.5275 Remote Similarity NPC473634
0.5275 Remote Similarity NPC138811
0.5238 Remote Similarity NPC259152
0.5238 Remote Similarity NPC603782
0.5213 Remote Similarity NPC124155
0.5181 Remote Similarity NPC183357
0.5176 Remote Similarity NPC73511
0.5161 Remote Similarity NPC46202
0.5158 Remote Similarity NPC488089
0.5143 Remote Similarity NPC14958
0.5116 Remote Similarity NPC27942
0.5116 Remote Similarity NPC599850
0.5059 Remote Similarity NPC64305
0.5059 Remote Similarity NPC277205
0.5059 Remote Similarity NPC37919
0.5059 Remote Similarity NPC136042
0.5057 Remote Similarity NPC479401
0.5057 Remote Similarity NPC285197
0.5054 Remote Similarity NPC204693
0.5053 Remote Similarity NPC473623

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC82905 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
0.5684 Remote Similarity NPD7472 Pre-clinical

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