Structure

Physi-Chem Properties

Molecular Weight:  396.3
Volume:  436.517
LogP:  6.473
LogD:  4.93
LogS:  -6.231
# Rotatable Bonds:  0
TPSA:  18.46
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  6
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.464
Synthetic Accessibility Score:  5.377
Fsp3:  0.852
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.88
MDCK Permeability:  1.956737287400756e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.983
30% Bioavailability (F30%):  0.235

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.182
Plasma Protein Binding (PPB):  97.17667388916016%
Volume Distribution (VD):  2.148
Pgp-substrate:  1.7126103639602661%

ADMET: Metabolism

CYP1A2-inhibitor:  0.104
CYP1A2-substrate:  0.518
CYP2C19-inhibitor:  0.342
CYP2C19-substrate:  0.92
CYP2C9-inhibitor:  0.364
CYP2C9-substrate:  0.057
CYP2D6-inhibitor:  0.393
CYP2D6-substrate:  0.664
CYP3A4-inhibitor:  0.912
CYP3A4-substrate:  0.663

ADMET: Excretion

Clearance (CL):  11.262
Half-life (T1/2):  0.093

ADMET: Toxicity

hERG Blockers:  0.995
Human Hepatotoxicity (H-HT):  0.479
Drug-inuced Liver Injury (DILI):  0.453
AMES Toxicity:  0.038
Rat Oral Acute Toxicity:  0.348
Maximum Recommended Daily Dose:  0.712
Skin Sensitization:  0.99
Carcinogencity:  0.519
Eye Corrosion:  0.754
Eye Irritation:  0.511
Respiratory Toxicity:  0.975

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  Natural Product: NPC218199

Natural Product ID:  NPC218199
Common Name*:   YEQBGJNMHDZXRG-ASBKZRTJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YEQBGJNMHDZXRG-ASBKZRTJSA-N
Standard InCHI:  InChI=1S/C27H40O2/c1-17-10-14-27(28-16-17)18(2)24-23(29-27)15-22-20-9-8-19-7-5-6-12-25(19,3)21(20)11-13-26(22,24)4/h5,7-8,17-18,20-24H,6,9-16H2,1-4H3/t17-,18+,20-,21+,22+,23+,24+,25+,26+,27-/m1/s1
SMILES:  C[C@@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC=C6C=CCC[C@]6(C)[C@H]5CC[C@]34C)O2)OC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   337494
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

*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
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruit n.a. n.a. DOI[10.1016/S0963-9969(99)00095-2]
NPO22018 Hydrangea chinensis Species Hydrangeaceae Eukaryota Roots n.a. n.a. PMID[11473431]
NPO20244 Melicope semecarpifolia Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[11575945]
NPO20244 Melicope semecarpifolia Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[18163582]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota n.a. fruit n.a. PMID[21648406]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota rhizomes n.a. n.a. PMID[23707257]
NPO26918 Taricha granulosa Species Salamandridae Eukaryota n.a. n.a. n.a. PMID[32896120]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruit Juice n.a. n.a. Database[FooDB]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23313 Dioscorea althaeoides Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27509 Dioscorea zingiberensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4863 Dioscorea futschauensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31560 Dioscorea hypoglauca Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6532 Lithospermum ruderale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22018 Hydrangea chinensis Species Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15018 Dioscorea collettii Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14297 Dioscorea gracillima Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17650 Dioscorea septemloba Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20244 Melicope semecarpifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15886 Lepidium campestre Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO6532 Lithospermum ruderale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17650 Dioscorea septemloba Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23313 Dioscorea althaeoides Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15886 Lepidium campestre Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22018 Hydrangea chinensis Species Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27509 Dioscorea zingiberensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4863 Dioscorea futschauensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO127 Phragmites australis Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20244 Melicope semecarpifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15018 Dioscorea collettii Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14297 Dioscorea gracillima Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO31560 Dioscorea hypoglauca Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30856 Oioscorea parviflora n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15018 Dioscorea collettii Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23313 Dioscorea althaeoides Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30749 Dioscorea panthalca Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27509 Dioscorea zingiberensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4863 Dioscorea futschauensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14297 Dioscorea gracillima Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17650 Dioscorea septemloba Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO127 Phragmites australis Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17650 Dioscorea septemloba Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4863 Dioscorea futschauensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23067 Shorea maranti Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27509 Dioscorea zingiberensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12967 Reseda suffruticosa Species Resedaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15886 Lepidium campestre Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23313 Dioscorea althaeoides Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15018 Dioscorea collettii Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17650 Dioscorea septemloba Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1463 Corethrodendron scoparium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22402 Lupinus mutabilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17338 Solanum asperum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20565 Aplysina fulva Species Aplysinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20244 Melicope semecarpifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22018 Hydrangea chinensis Species Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19482 Tapinoma nigerrimum Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14409 Dioscorea nipponica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7802 Dacrycarpus vieillardii Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22836 Alpinia mutica Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6532 Lithospermum ruderale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23001 Halimium umbellatum Species Cistaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3347 Vaccinium corymbosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4863 Dioscorea futschauensis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20402 Ageratina gilbertii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14902 Pteris marginata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14627 Caloscypha fulgens Species Caloscyphaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18364 Genista lusitanica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16398 Nicotiana alata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26918 Taricha granulosa Species Salamandridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14297 Dioscorea gracillima Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO127 Phragmites australis Species Poaceae 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 NPC218199 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 NPC218199 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