Structure

Physi-Chem Properties

Molecular Weight:  624.35
Volume:  619.405
LogP:  2.348
LogD:  2.442
LogS:  -3.22
# Rotatable Bonds:  8
TPSA:  178.67
# H-Bond Aceptor:  11
# H-Bond Donor:  6
# Rings:  6
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.13
Synthetic Accessibility Score:  6.39
Fsp3:  0.909
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.583
MDCK Permeability:  9.200115164276212e-05
Pgp-inhibitor:  0.963
Pgp-substrate:  0.762
Human Intestinal Absorption (HIA):  0.911
20% Bioavailability (F20%):  0.351
30% Bioavailability (F30%):  0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.029
Plasma Protein Binding (PPB):  67.64173126220703%
Volume Distribution (VD):  0.629
Pgp-substrate:  18.143888473510742%

ADMET: Metabolism

CYP1A2-inhibitor:  0.006
CYP1A2-substrate:  0.092
CYP2C19-inhibitor:  0.008
CYP2C19-substrate:  0.442
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.026
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.048
CYP3A4-inhibitor:  0.275
CYP3A4-substrate:  0.151

ADMET: Excretion

Clearance (CL):  1.992
Half-life (T1/2):  0.785

ADMET: Toxicity

hERG Blockers:  0.097
Human Hepatotoxicity (H-HT):  0.204
Drug-inuced Liver Injury (DILI):  0.212
AMES Toxicity:  0.074
Rat Oral Acute Toxicity:  0.566
Maximum Recommended Daily Dose:  0.038
Skin Sensitization:  0.107
Carcinogencity:  0.441
Eye Corrosion:  0.003
Eye Irritation:  0.012
Respiratory Toxicity:  0.984

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General Info & Identifiers & Properties  
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Similar NPs/Drugs  

  Natural Product: NPC184181

Natural Product ID:  NPC184181
Common Name*:   LQTHAYNKWCIXET-PIZJTGSRSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LQTHAYNKWCIXET-PIZJTGSRSA-N
Standard InCHI:  InChI=1S/C33H52O11/c1-15(20(13-32(6,40)30(3,4)39)41-29-26(38)25(37)24(36)21(14-34)42-29)18-7-8-19-23-17(9-11-31(18,19)5)16(2)33(28-27(23)43-28)12-10-22(35)44-33/h9,15-16,18-21,23-29,34,36-40H,7-8,10-14H2,1-6H3/t15-,16-,18+,19-,20+,21+,23+,24+,25-,26+,27-,28-,29+,31+,32+,33+/m0/s1
SMILES:  C[C@@H]([C@H]1CC[C@H]2[C@H]3C(=CC[C@]12C)[C@H](C)[C@]1(CCC(=O)O1)[C@@H]1[C@H]3O1)[C@@H](C[C@](C)(C(C)(C)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides

*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.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota aerial parts n.a. n.a. PMID[11087596]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota underground parts n.a. n.a. PMID[12398537]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota fresh tubers n.a. n.a. PMID[14738376]
NPO9060 Sinularia granosa Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[18831569]
NPO9060 Sinularia granosa Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[22672798]
NPO16831 Hypericum patulum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[31999455]
NPO16831 Hypericum patulum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14012 Libanotis condensata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14012 Libanotis condensata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16831 Hypericum patulum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15843 Dalbergia retusa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22329 Dolomedes okefinokensis Species Pisauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13354 Euryspongia arenaria Species Dysideidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15843 Dalbergia retusa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13502 Senecio algens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14346 Pterocarpus indica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12106 Aristeomorpha foliacea Species Aristeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13841 Allium minutiflorum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2991 Duboisia leichhardtii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15742 Euphorbia laurifolia Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12655 Tephrosia virginiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16338 Virola calophylloidea Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15121 Solanum habrochaites Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16150 Nepeta argolica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10741 Eucalyptus grossa Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16260 Stevia yaconensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16498 Adoxophyes orana Species Tortricidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1069 Meum athamanticum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7342 Bostrychia scorpioides Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14012 Libanotis condensata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14968 Mucuna membranacea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16574 Heywoodiella oligocephala n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11547 Lobelia cardinalis Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16417 Elaeocarpus ganitrus Species Elaeocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2295 Cydonia vulgaris Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4167 Oxalis repens Species Oxalidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9060 Sinularia granosa Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2725 Casuarina glauca Species Casuarinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14531 Dalbergia inundata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16053 Allium aflatunense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9540 Curvularia falcata Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13204 Mallotus metcalfianus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16537 Lonicera racemosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11780 Alpinia rafflesiana Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3247 Orchis fusca Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16831 Hypericum patulum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15838 Psorospermum molluscum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1337 Sphyraena japonica Species Sphyraenidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14704 Ephedra frustillata Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24523 Senecio anteuphorbium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5115 Abuta panurensis Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4793 Discoglossus pictus Species Alytidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14167 Ambrosia artemisioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15377 Calea clematidea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13686 Lepraria lobificans Species Stereocaulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6380 Hydrocotyle vulgaris Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15615 Petunia hybrid Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8288 Vitis cinerea Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7540 Eucalyptus consideniana Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15232 Absidia repens Species Cunninghamellaceae 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 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].

  Biological Activity

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.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

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 NPC184181 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

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC184181 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: Similar Natural Products in NPASS

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