Structure

Physi-Chem Properties

Molecular Weight:  218.17
Volume:  245.844
LogP:  2.882
LogD:  3.224
LogS:  -2.433
# Rotatable Bonds:  2
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.706
Synthetic Accessibility Score:  4.938
Fsp3:  0.733
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.38
MDCK Permeability:  1.5872259609750472e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.257
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.759
30% Bioavailability (F30%):  0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.855
Plasma Protein Binding (PPB):  45.271568298339844%
Volume Distribution (VD):  1.583
Pgp-substrate:  63.13264846801758%

ADMET: Metabolism

CYP1A2-inhibitor:  0.61
CYP1A2-substrate:  0.293
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.787
CYP2C9-inhibitor:  0.017
CYP2C9-substrate:  0.051
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.112
CYP3A4-inhibitor:  0.374
CYP3A4-substrate:  0.267

ADMET: Excretion

Clearance (CL):  13.412
Half-life (T1/2):  0.446

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.145
Drug-inuced Liver Injury (DILI):  0.723
AMES Toxicity:  0.035
Rat Oral Acute Toxicity:  0.938
Maximum Recommended Daily Dose:  0.649
Skin Sensitization:  0.432
Carcinogencity:  0.885
Eye Corrosion:  0.273
Eye Irritation:  0.529
Respiratory Toxicity:  0.973

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC98340

Natural Product ID:  NPC98340
Common Name*:   RYPZBJYEIAAUNP-WCDYYPSBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RYPZBJYEIAAUNP-WCDYYPSBSA-N
Standard InCHI:  InChI=1S/C15H22O/c1-9-4-5-15(3,10(9)2)14-7-12-11(8-16)6-13(12)14/h6,10,12-14,16H,1,4-5,7-8H2,2-3H3/t10-,12+,13-,14-,15+/m0/s1
SMILES:  C=C1CC[C@](C)([C@H]1C)[C@H]1C[C@@H]2C(=C[C@H]12)CO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0000286] Primary alcohols

*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
NPO14922 Tarenna attenuata Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[16792422]
NPO14922 Tarenna attenuata Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[17343407]
NPO8996 Aplysina gerardogreeni Species Aplysinidae Eukaryota n.a. n.a. n.a. PMID[17512741]
NPO17974 Sarcophyton subviride Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[27704808]
NPO19344 Sporormiella teretispora Species Sporormiaceae Eukaryota n.a. n.a. n.a. PMID[7760082]
NPO18477 Celastrus scandens Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18640 Tectona grandis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18308 Saponaria officinalis Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13137 Isodon flexicaulis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18308 Saponaria officinalis Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19480 Laurencia nipponica Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18640 Tectona grandis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3608 Eleutherococcus giraldii Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18477 Celastrus scandens Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18640 Tectona grandis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15695 Mikania vitifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18964 Iva hayesiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19739 Astragalus alexandri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19344 Sporormiella teretispora Species Sporormiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16666 Eunicea calyculata Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28880 Aquilegia coerulea Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17309 Halfordia scleroxyla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16892 Helogyne hutchisonii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO18394 Linaria purpurea Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22229 Alternaria botrytis Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27685 Abuta concolor Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8996 Aplysina gerardogreeni Species Aplysinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19544 Camassia cusickii Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17173 Sporobolus alterniflorus Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17974 Sarcophyton subviride Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16219 Hyssopus lophanthoides Species Eulophidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19053 Pteris formosana Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18308 Saponaria officinalis Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10706 Bergenia hissarica Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18640 Tectona grandis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16010 Synoicum prunum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18477 Celastrus scandens Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17546 Torulaspora delbrueckii Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20433 Garuga gamblei Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3608 Eleutherococcus giraldii Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19480 Laurencia nipponica Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3680 Beilschmiedia obtusifolia Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14922 Tarenna attenuata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18891 Stevia potrerensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1550 Talaromyces purpureogenus Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12767 Cassipourea gummiflua Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19140 Aloe excelsa Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7040 Sinularia parva Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14030 Alcyonium paessleri Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14511 Lespedeza striata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO647 Rhodotorula glutinis Species Sporidiobolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18567 Salvia clevelandi Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27736 Melanochromis auratus Species Cichlidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3628 Solanum aethiopicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17672 Euryops linifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13137 Isodon flexicaulis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1998 Premna serratifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13566 Hypoxylon serpens Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14318 Lespedeza davidii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25617 Lactococcus lactis Species Streptococcaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10038.2 Abies pinsapo var. tazaotana Varieties Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16528 Psydrax dicoccos Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17559 Coespeletia lutescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17429 Teucrium creticum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1192 Salvia corrugata Species Lamiaceae 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 NPC98340 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 NPC98340 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