Structure

Physi-Chem Properties

Molecular Weight:  338.12
Volume:  343.11
LogP:  3.675
LogD:  3.179
LogS:  -5.914
# Rotatable Bonds:  2
TPSA:  73.58
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.588
Synthetic Accessibility Score:  3.599
Fsp3:  0.35
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.813
MDCK Permeability:  2.2006222934578545e-05
Pgp-inhibitor:  0.462
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.041

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.017
Plasma Protein Binding (PPB):  98.06201171875%
Volume Distribution (VD):  1.539
Pgp-substrate:  1.464858055114746%

ADMET: Metabolism

CYP1A2-inhibitor:  0.932
CYP1A2-substrate:  0.927
CYP2C19-inhibitor:  0.889
CYP2C19-substrate:  0.107
CYP2C9-inhibitor:  0.77
CYP2C9-substrate:  0.731
CYP2D6-inhibitor:  0.401
CYP2D6-substrate:  0.562
CYP3A4-inhibitor:  0.855
CYP3A4-substrate:  0.299

ADMET: Excretion

Clearance (CL):  5.054
Half-life (T1/2):  0.034

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.62
Drug-inuced Liver Injury (DILI):  0.915
AMES Toxicity:  0.463
Rat Oral Acute Toxicity:  0.808
Maximum Recommended Daily Dose:  0.393
Skin Sensitization:  0.171
Carcinogencity:  0.855
Eye Corrosion:  0.003
Eye Irritation:  0.017
Respiratory Toxicity:  0.198

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC290249

Natural Product ID:  NPC290249
Common Name*:   YFDKIHAZVQFLRC-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YFDKIHAZVQFLRC-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C20H18O5/c1-10-9-25-18-12-6-7-13-11(15(12)17(22)16(21)14(10)18)5-4-8-20(13,2)19(23)24-3/h6-7,9H,4-5,8H2,1-3H3
SMILES:  Cc1coc2-c3ccc4c(CCCC4(C)C(=O)OC)c3C(=O)C(=O)c12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   624381
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]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[11473439]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[12141863]
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]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20515057]
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]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27947 Salvia flava Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2385 Salvia bowleyana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19925 Salvia sinica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25813.1 Salvia przewalskii var. mandarinorum Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16750 Salvia castanea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18449 Salvia yunnanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14213 Salvia bulleyana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18449 Salvia yunnanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16259.1 Syringa reticulata subsp. amurensis Subspecies Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25813.1 Salvia przewalskii var. mandarinorum Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14213 Salvia bulleyana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2385 Salvia bowleyana 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]
NPO16750 Salvia castanea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19925 Salvia sinica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27947 Salvia flava Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19451 Salvia prionitis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5743 Salvia miltiorrhiza Species Lamiaceae 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]
NPO14979 Salvia trijuga Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16750 Salvia castanea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27947 Salvia flava Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16259.1 Syringa reticulata subsp. amurensis Subspecies Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18449 Salvia yunnanensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26049 Salvia digitaloides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19451 Salvia prionitis 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 NPC290249 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 NPC290249 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