Structure

Physi-Chem Properties

Molecular Weight:  296.1
Volume:  302.364
LogP:  2.99
LogD:  2.547
LogS:  -5.094
# Rotatable Bonds:  0
TPSA:  67.51
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.758
Synthetic Accessibility Score:  3.571
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  2

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.741
MDCK Permeability:  2.0108096578042023e-05
Pgp-inhibitor:  0.265
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.167

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.067
Plasma Protein Binding (PPB):  95.55548858642578%
Volume Distribution (VD):  1.941
Pgp-substrate:  3.7084600925445557%

ADMET: Metabolism

CYP1A2-inhibitor:  0.931
CYP1A2-substrate:  0.821
CYP2C19-inhibitor:  0.386
CYP2C19-substrate:  0.067
CYP2C9-inhibitor:  0.442
CYP2C9-substrate:  0.239
CYP2D6-inhibitor:  0.466
CYP2D6-substrate:  0.262
CYP3A4-inhibitor:  0.846
CYP3A4-substrate:  0.192

ADMET: Excretion

Clearance (CL):  6.023
Half-life (T1/2):  0.039

ADMET: Toxicity

hERG Blockers:  0.069
Human Hepatotoxicity (H-HT):  0.555
Drug-inuced Liver Injury (DILI):  0.823
AMES Toxicity:  0.632
Rat Oral Acute Toxicity:  0.781
Maximum Recommended Daily Dose:  0.886
Skin Sensitization:  0.141
Carcinogencity:  0.939
Eye Corrosion:  0.004
Eye Irritation:  0.114
Respiratory Toxicity:  0.881

Download Data

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

  Natural Product: NPC270476

Natural Product ID:  NPC270476
Common Name*:   JVRKHBLVECIWMZ-SFHVURJKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JVRKHBLVECIWMZ-SFHVURJKSA-N
Standard InCHI:  InChI=1S/C18H16O4/c1-9-8-22-17-11-5-6-12-10(4-3-7-18(12,2)21)14(11)16(20)15(19)13(9)17/h5-6,8,21H,3-4,7H2,1-2H3/t18-/m0/s1
SMILES:  Cc1coc2-c3ccc4c(CCC[C@]4(C)O)c3C(=O)C(=O)c12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   56967683
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0002548] Tanshinones, isotanshinones, and derivatives

*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
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[11374966]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[12880325]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[1567426]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[16038550]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[17217287]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17583950]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18855446]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20455578]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21775156]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23286284]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24108414]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27569393]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29185738]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30351923]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[3655791]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota roots n.a. n.a. PMID[9834151]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24740 Uvaria klaineana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28257 Dioscorea communis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12800 Glycine falcata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26054 Palmaria palmata Species Palmariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24740 Uvaria klaineana Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23960 Artemisia siversiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25868 Decachaeta ovatifolia n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26087 Euphorbia retusa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27437 Camptothecium lutescens Species Brachytheciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25212 Ritterella rubra n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28257 Dioscorea communis Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10155 Stauntonia obovatifoliola Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25701 Amentotaxus yunnanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26223 Cladonia bellidiflora Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12476 Delphinium cyphoplectrum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23417 Rhabdia lycioides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26316 Pleurophycus gardneri Species Alariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6346 Phallusia fumigata Species Ascidiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25779 Vicia sativa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25974 Streptomyces lateritius Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6321 Agathosma thymifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO415 Deguelia hatschbachii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24988 Viburnum sieboldi Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22758 Picradeniopsis pringlei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10497 Hydrolithon reinboldii Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4009 Allochromatium minutissimum Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22016 0tholaena dealbata Species Pteridaceae 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 NPC270476 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 NPC270476 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