Structure

Physi-Chem Properties

Molecular Weight:  312.3
Volume:  369.42
LogP:  6.04
LogD:  5.129
LogS:  -4.672
# Rotatable Bonds:  14
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.425
Synthetic Accessibility Score:  3.671
Fsp3:  0.9
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.456
MDCK Permeability:  1.3675536138180178e-05
Pgp-inhibitor:  0.046
Pgp-substrate:  0.202
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.996
30% Bioavailability (F30%):  0.537

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.381
Plasma Protein Binding (PPB):  94.3869400024414%
Volume Distribution (VD):  0.981
Pgp-substrate:  3.511162519454956%

ADMET: Metabolism

CYP1A2-inhibitor:  0.313
CYP1A2-substrate:  0.18
CYP2C19-inhibitor:  0.184
CYP2C19-substrate:  0.063
CYP2C9-inhibitor:  0.543
CYP2C9-substrate:  0.793
CYP2D6-inhibitor:  0.039
CYP2D6-substrate:  0.058
CYP3A4-inhibitor:  0.05
CYP3A4-substrate:  0.11

ADMET: Excretion

Clearance (CL):  8.784
Half-life (T1/2):  0.152

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.169
Drug-inuced Liver Injury (DILI):  0.289
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.068
Maximum Recommended Daily Dose:  0.403
Skin Sensitization:  0.812
Carcinogencity:  0.404
Eye Corrosion:  0.164
Eye Irritation:  0.492
Respiratory Toxicity:  0.919

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  Natural Product: NPC181366

Natural Product ID:  NPC181366
Common Name*:   KDJDYRMHRJLXAB-CMKODMSKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KDJDYRMHRJLXAB-CMKODMSKSA-N
Standard InCHI:  InChI=1S/C20H40O2/c1-16(2)9-6-10-17(3)11-7-12-18(4)13-8-14-19(5)20(22)15-21/h16-18,20-22H,5-15H2,1-4H3/t17-,18-,20+/m0/s1
SMILES:  CC(C)CCC[C@H](C)CCC[C@H](C)CCCC(=C)[C@@H](CO)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:0001551] Diterpenoids
          • [CHEMONTID:0001357] Acyclic diterpenoids

*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
NPO19965 Helenium alternifolium Species Asteraceae Eukaryota n.a. aerial part n.a. DOI[10.1021/jo01271a036]
NPO21850 Paeonia delavayi Species Paeoniaceae Eukaryota n.a. root n.a. PMID[10945272]
NPO23006 Moringa stenopetala Species Moringaceae Eukaryota n.a. n.a. n.a. PMID[12709911]
NPO22820 Sarcophyton glaucum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[15332846]
NPO22820 Sarcophyton glaucum Species Alcyoniidae Eukaryota n.a. Amami Oshima, Kagoshima Prefecture, Japan n.a. PMID[16933862]
NPO22820 Sarcophyton glaucum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[19331379]
NPO22820 Sarcophyton glaucum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[21563811]
NPO20835 Medicago truncatula Species Fabaceae Eukaryota n.a. root n.a. PMID[21615146]
NPO21278 Lysimachia clethroides Species Primulaceae Eukaryota n.a. aerial part n.a. PMID[21928797]
NPO21850 Paeonia delavayi Species Paeoniaceae Eukaryota n.a. seed n.a. PMID[23497864]
NPO22372 Callicarpa bodinieri Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29578342]
NPO14240 Justicia ghiesbreghtiana Species Acanthaceae Eukaryota n.a. n.a. n.a. PMID[9748395]
NPO12807 Citrus aurantiifolia Species Rutaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO12807 Citrus aurantiifolia Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO12807 Citrus aurantiifolia Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO12807 Citrus aurantiifolia Species Rutaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO21343 Eupatorium fortunei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21221 Trapa bispinosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21850 Paeonia delavayi Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12807 Citrus aurantiifolia Species Rutaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO12807 Citrus aurantiifolia Species Rutaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO12807 Citrus aurantiifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21221 Trapa bispinosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15763 Huperzia lucidula Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21850 Paeonia delavayi Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21278 Lysimachia clethroides Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15478 Senna sophera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22438 Asclepias speciosa Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21343 Eupatorium fortunei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21413 Armillaria tabescens Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21343 Eupatorium fortunei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21221 Trapa bispinosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20021 Physcia aegialita Species Physciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21089 Mourera fluviatilis Species Podostemaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22499 Corydalis flabellata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21413 Armillaria tabescens Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22820 Sarcophyton glaucum Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20381 Echites hirsuta Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28103 Erica carnea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20967 Doriopsilla albopunctata Species Dendrodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21599 Ricciocarpos natans Species Ricciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22048 Pteris palmiformis Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18123 Dichapetalum madagascariense Species Dichapetalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20835 Medicago truncatula Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23006 Moringa stenopetala Species Moringaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20771 Thalictrum fortunei Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22698 Achillea pannonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22113 Anthocercis genistoides Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19965 Helenium alternifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21221 Trapa bispinosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22308 Stevia satureiaefolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14240 Justicia ghiesbreghtiana Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12807 Citrus aurantiifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15763 Huperzia lucidula Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22953 Eupatorium pauciflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22756 Epimedium versicolor Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22438 Asclepias speciosa Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21158 Viburnum fur Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21032 Manilkara hexandra Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21850 Paeonia delavayi Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20707 Stillingia sanguinolenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27929 Aphanamixis polystachya Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8115 Polyopes affinis Species Halymeniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22372 Callicarpa bodinieri Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13409 Crocus asturicus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20896 Mimosa tenuiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20203 Syringa komarowi Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20522 Pyura sacciformis Species Pyuridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27489 Alloascoidea hylecoeti Species Alloascoideaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21654 Cyerce cristallina Species Caliphyllidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22887 Scutellaria violacea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15478 Senna sophera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20261 Teucrium trifidum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20583 Phaulopsis imbricata Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21725 Uncaria glabrata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4478 Parmelia pseudoreticulata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20088 Piper sintenense Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21343 Eupatorium fortunei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20457 Spirastrella inconstans Species Spirastrellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21278 Lysimachia clethroides Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26325 Annulusmagnus triseptatus Species Annulatascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19891 Diospyros crassiflora Species Ebenaceae 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 NPC181366 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 NPC181366 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