Molecular Weight:   | 754.49 |
Volume:   | 769.199 |
LogP:   | 3.627 |
LogD:   | 3.943 |
LogS:   | -3.738 |
# Rotatable Bonds:   | 9 |
TPSA:   | 198.76 |
# H-Bond Aceptor:   | 12 |
# H-Bond Donor:   | 8 |
# Rings:   | 6 |
# Heavy Atoms:   | 12 |
QED Drug-Likeness Score:   | 0.161 |
Synthetic Accessibility Score:   | 5.876 |
Fsp3:   | 0.951 |
Lipinski Rule-of-5:   | Rejected |
Pfizer Rule:   | Accepted |
GSK Rule:   | Rejected |
BMS Rule:   | 1 |
Golden Triangle Rule:   | Rejected |
Chelating Alert:   | 0 |
PAINS Alert:   | 0 |
Caco-2 Permeability:   | -5.348 |
MDCK Permeability:   | 1.3047438187641092e-05 |
Pgp-inhibitor:   | 0.998 |
Pgp-substrate:   | 0.194 |
Human Intestinal Absorption (HIA):   | 0.698 |
20% Bioavailability (F20%):   | 0.164 |
30% Bioavailability (F30%):   | 0.972 |
Blood-Brain-Barrier Penetration (BBB):   | 0.007 |
Plasma Protein Binding (PPB):   | 83.57051086425781% |
Volume Distribution (VD):   | 0.432 |
Pgp-substrate:   | 8.676414489746094% |
CYP1A2-inhibitor:   | 0.001 |
CYP1A2-substrate:   | 0.299 |
CYP2C19-inhibitor:   | 0.002 |
CYP2C19-substrate:   | 0.458 |
CYP2C9-inhibitor:   | 0.01 |
CYP2C9-substrate:   | 0.027 |
CYP2D6-inhibitor:   | 0.007 |
CYP2D6-substrate:   | 0.108 |
CYP3A4-inhibitor:   | 0.018 |
CYP3A4-substrate:   | 0.037 |
Clearance (CL):   | 0.725 |
Half-life (T1/2):   | 0.517 |
hERG Blockers:   | 0.316 |
Human Hepatotoxicity (H-HT):   | 0.17 |
Drug-inuced Liver Injury (DILI):   | 0.006 |
AMES Toxicity:   | 0.035 |
Rat Oral Acute Toxicity:   | 0.197 |
Maximum Recommended Daily Dose:   | 0.786 |
Skin Sensitization:   | 0.947 |
Carcinogencity:   | 0.008 |
Eye Corrosion:   | 0.003 |
Eye Irritation:   | 0.016 |
Respiratory Toxicity:   | 0.909 |
Natural Product ID:   | NPC121648 |
Common Name*:   | YNBYFOIDLBTOMW-IPTBNLQOSA-N |
IUPAC Name:   | n.a. |
Synonyms:   | |
Standard InCHIKey:   | YNBYFOIDLBTOMW-IPTBNLQOSA-N |
Standard InCHI:   | InChI=1S/C41H70O12/c1-21(2)10-9-14-41(8,53-36-34(49)32(47)31(46)25(52-36)20-51-35-33(48)30(45)24(43)19-50-35)22-11-16-40(7)29(22)23(42)18-27-38(5)15-13-28(44)37(3,4)26(38)12-17-39(27,40)6/h10,22-36,42-49H,9,11-20H2,1-8H3/t22-,23+,24+,25+,26-,27+,28-,29-,30-,31+,32-,33+,34+,35-,36-,38-,39+,40+,41-/m0/s1 |
SMILES:   | CC(=CCC[C@@](C)([C@H]1CC[C@]2(C)[C@@H]1[C@@H](C[C@@H]1[C@@]3(C)CC[C@@H](C(C)(C)[C@@H]3CC[C@@]21C)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@@H](CO2)O)O)O)O1)O)O)O)C |
Synthetic Gene Cluster:   | n.a. |
ChEMBL Identifier:   | n.a. |
PubChem CID:   |
11331683 |
Chemical Classification**:   |
|
*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.
Organism ID | Organism Name | Taxonomy Level | Family | SuperKingdom | Isolation Part | Collection Location | Collection Time | Reference |
---|---|---|---|---|---|---|---|---|
NPO28011 | Swertia japonica | Species | Gentianaceae | Eukaryota | n.a. | n.a. | n.a. | DOI[10.1007/BF02675902] |
NPO11144 | Centella asiatica | Species | Apiaceae | Eukaryota | n.a. | n.a. | n.a. | DOI[10.1007/s11816-015-0350-y] |
NPO28011 | Swertia japonica | Species | Gentianaceae | Eukaryota | n.a. | n.a. | n.a. | DOI[10.1055/s-2008-1074888] |
NPO28011 | Swertia japonica | Species | Gentianaceae | Eukaryota | n.a. | n.a. | n.a. | DOI[10.1248/cpb.30.4088] |
NPO28011 | Swertia japonica | Species | Gentianaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[10353265] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[10553679] |
NPO22175 | Perovskia abrotanoides | Species | Lamiaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[11720520] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[12055308] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[15070765] |
NPO28035 | Streptomyces fumanus | Species | Streptomycetaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[15730262] |
NPO28391 | Euonymus nanoides | Species | Celastraceae | Eukaryota | n.a. | seed | n.a. |
PMID[16462067] |
NPO11144 | Centella asiatica | Species | Apiaceae | Eukaryota | n.a. | aerial part | n.a. |
PMID[17520525] |
NPO28528 | Bridelia ferruginea | Species | Phyllanthaceae | Eukaryota | roots | Gabon | 1987 |
PMID[18327911] |
NPO28528 | Bridelia ferruginea | Species | Phyllanthaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[18327911] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[19276083] |
NPO12934 | Gynostemma pentaphyllum | Species | Cucurbitaceae | Eukaryota | Stems | n.a. | n.a. |
PMID[20104880] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[20448045] |
NPO10946 | Pseudallescheria boydii | Species | Microascaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[20509707] |
NPO28217 | Septoria pistaciarum | Species | Mycosphaerellaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[20550123] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[20843794] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[22194604] |
NPO12934 | Gynostemma pentaphyllum | Species | Cucurbitaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[22342101] |
NPO28217 | Septoria pistaciarum | Species | Mycosphaerellaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[22530813] |
NPO11144 | Centella asiatica | Species | Apiaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[22966846] |
NPO10946 | Pseudallescheria boydii | Species | Microascaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[23964677] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[24516143] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[25028392] |
NPO12934 | Gynostemma pentaphyllum | Species | Cucurbitaceae | Eukaryota | aerial parts | n.a. | n.a. |
PMID[25895106] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[26466957] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[26774486] |
NPO28528 | Bridelia ferruginea | Species | Phyllanthaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[26938998] |
NPO28011 | Swertia japonica | Species | Gentianaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[26996316] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[27242221] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[27807341] |
NPO28011 | Swertia japonica | Species | Gentianaceae | Eukaryota | n.a. | n.a. | n.a. |
PMID[5583807] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[8917504] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. |
PMID[97292] |
NPO28334 | Pyrola decorata | Species | Ericaceae | Eukaryota | n.a. | n.a. | n.a. | Database[HerDing] |
NPO28011 | Swertia japonica | Species | Gentianaceae | Eukaryota | n.a. | n.a. | n.a. | Database[HerDing] |
NPO28576 | Berberis julianae | Species | Berberidaceae | Eukaryota | n.a. | n.a. | n.a. | Database[HerDing] |
NPO11990 | Coleostephus myconis | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[HerDing] |
NPO12934 | Gynostemma pentaphyllum | Species | Cucurbitaceae | Eukaryota | n.a. | n.a. | n.a. | Database[HerDing] |
NPO11144 | Centella asiatica | Species | Apiaceae | Eukaryota | n.a. | n.a. | n.a. | Database[HerDing] |
NPO918 | Dahlia pinnata | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[HerDing] |
NPO11144 | Centella asiatica | Species | Apiaceae | Eukaryota | n.a. | n.a. | n.a. | Database[MetaboLights] |
NPO918 | Dahlia pinnata | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCMID] |
NPO28576 | Berberis julianae | Species | Berberidaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCMID] |
NPO11144 | Centella asiatica | Species | Apiaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCMID] |
NPO28334 | Pyrola decorata | Species | Ericaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCMID] |
NPO12934 | Gynostemma pentaphyllum | Species | Cucurbitaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCMID] |
NPO12450 | Cneorum pulverulentum | Species | Rutaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCMID] |
NPO28011 | Swertia japonica | Species | Gentianaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCMID] |
NPO11990 | Coleostephus myconis | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCMID] |
NPO28334 | Pyrola decorata | Species | Ericaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCM_Taiwan] |
NPO12934 | Gynostemma pentaphyllum | Species | Cucurbitaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCM_Taiwan] |
NPO11990 | Coleostephus myconis | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCM_Taiwan] |
NPO28576 | Berberis julianae | Species | Berberidaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCM_Taiwan] |
NPO11144 | Centella asiatica | Species | Apiaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCM_Taiwan] |
NPO28011 | Swertia japonica | Species | Gentianaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TCM_Taiwan] |
NPO28011 | Swertia japonica | Species | Gentianaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TM-MC] |
NPO11144 | Centella asiatica | Species | Apiaceae | Eukaryota | n.a. | n.a. | n.a. | Database[TM-MC] |
NPO27959 | Codonocarpus australis | Species | Gyrostemonaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO29353 | Benzoin praecox | n.a. | n.a. | n.a. | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28035 | Streptomyces fumanus | Species | Streptomycetaceae | Bacteria | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28528 | Bridelia ferruginea | Species | Phyllanthaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28614 | Zieria smithii | Species | Rutaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28633 | Bystropogon origanifolius | Species | Lamiaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28334 | Pyrola decorata | Species | Ericaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28596 | Streptomyces lavendofoliae | Species | Streptomycetaceae | Bacteria | n.a. | n.a. | n.a. | Database[UNPD] |
NPO11144 | Centella asiatica | Species | Apiaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28670 | Mortierella elongata | Species | Mortierellaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28391 | Euonymus nanoides | Species | Celastraceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO12934 | Gynostemma pentaphyllum | Species | Cucurbitaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO4305 | Pertusaria wulfenii | Species | Pertusariaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO25704 | Tetraneuris acaulis | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28374 | Pleogyne cunninghami | Species | Menispermaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO16506 | Synotis alata | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO6331 | Jacobaea subalpina | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28269 | Rubus rosa | Species | Rosaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28073 | Crateva nurvala | Species | Capparaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28509 | Achillea clypeolata | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO12450 | Cneorum pulverulentum | Species | Rutaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28200 | Unonopsis glaucopetala | Species | Annonaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28161 | Stephania sutchuenensis | Species | Menispermaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28217 | Septoria pistaciarum | Species | Mycosphaerellaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28691 | Streptomyces odorifer | Species | Streptomycetaceae | Bacteria | n.a. | n.a. | n.a. | Database[UNPD] |
NPO20081 | Mycobacterium tuberculosis | Species | Mycobacteriaceae | Bacteria | n.a. | n.a. | n.a. | Database[UNPD] |
NPO16669 | Diospyros verrucosa | Species | Ebenaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO27867 | Turbo argyrostoma | Species | Turbinidae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28704 | Agaricus hortensis | Species | Agaricaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28656 | Lactobacillus casei | Species | Lactobacillaceae | Bacteria | n.a. | n.a. | n.a. | Database[UNPD] |
NPO918 | Dahlia pinnata | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28481 | Cerbera dilatata | Species | Apocynaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28303 | Pleogyne cunninghamii | Species | Menispermaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28131 | Polygala amara | Species | Polygalaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO10946 | Pseudallescheria boydii | Species | Microascaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28011 | Swertia japonica | Species | Gentianaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO11990 | Coleostephus myconis | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28576 | Berberis julianae | Species | Berberidaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO27990 | Schizonepeta multifida | Species | Lamiaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO22175 | Perovskia abrotanoides | Species | Lamiaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO20395 | Athanasia crithmifolia | Species | Asteraceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO27943 | Cardamine pinnata | Species | Brassicaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO28053 | Quercus serrata | Species | Fagaceae | Eukaryota | n.a. | n.a. | n.a. | Database[UNPD] |
NPO29115 | Rhinella arenarum | Species | Bufonidae | 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].
Organism ID | NP ID | 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].
Target ID | Target Type | Target Name | Target Organism | Activity Type | Activity Relation | Value | Unit | Reference |
---|
☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.
Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)
Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient
●  The left chart: Distribution of similarity level between NPC121648 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).
Similarity Score | Similarity Level | Natural Product ID |
---|
Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.
●  The left chart: Distribution of similarity level between NPC121648 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).
Similarity Score | Similarity Level | Drug ID | Developmental Stage |
---|
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.