Structure

Physi-Chem Properties

Molecular Weight:  344.16
Volume:  351.019
LogP:  3.738
LogD:  2.354
LogS:  -3.908
# Rotatable Bonds:  1
TPSA:  83.83
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.602
Synthetic Accessibility Score:  4.862
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.723
MDCK Permeability:  2.201487404818181e-05
Pgp-inhibitor:  0.189
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.075

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.289
Plasma Protein Binding (PPB):  99.2579345703125%
Volume Distribution (VD):  0.436
Pgp-substrate:  1.6082167625427246%

ADMET: Metabolism

CYP1A2-inhibitor:  0.092
CYP1A2-substrate:  0.764
CYP2C19-inhibitor:  0.474
CYP2C19-substrate:  0.727
CYP2C9-inhibitor:  0.772
CYP2C9-substrate:  0.865
CYP2D6-inhibitor:  0.12
CYP2D6-substrate:  0.31
CYP3A4-inhibitor:  0.4
CYP3A4-substrate:  0.408

ADMET: Excretion

Clearance (CL):  1.262
Half-life (T1/2):  0.165

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.245
Drug-inuced Liver Injury (DILI):  0.179
AMES Toxicity:  0.092
Rat Oral Acute Toxicity:  0.822
Maximum Recommended Daily Dose:  0.121
Skin Sensitization:  0.776
Carcinogencity:  0.072
Eye Corrosion:  0.003
Eye Irritation:  0.691
Respiratory Toxicity:  0.061

Download Data

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

  Natural Product: NPC223573

Natural Product ID:  NPC223573
Common Name*:   SWVDNEGGBBYXGS-UWVAXJGDSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SWVDNEGGBBYXGS-UWVAXJGDSA-N
Standard InCHI:  InChI=1S/C20H24O5/c1-9(2)10-8-11-12(15(23)13(10)21)20-7-5-6-19(3,4)17(20)16(14(11)22)25-18(20)24/h8-9,16-17,21,23H,5-7H2,1-4H3/t16-,17+,20+/m1/s1
SMILES:  CC(C)c1cc2c(c(c1O)O)[C@@]13CCCC(C)(C)[C@@H]1[C@@H](C2=O)OC3=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   13966127
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001538] Diterpene lactones

*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
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[10096857]
NPO17119 Dalea versicolor Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[15043439]
NPO18606 Achyrocline bogotensis Species Asteraceae Eukaryota n.a. Colombian n.a. PMID[15844937]
NPO3291 Cynanchum auriculatum Species Apocynaceae Eukaryota n.a. root n.a. PMID[18401845]
NPO17362 Alstonia yunnanensis Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[19775092]
NPO18055 Isodon adenolomus Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[21534539]
NPO18055 Isodon adenolomus Species Lamiaceae Eukaryota aerial parts Shangrila, Yunnan Province, China 2008-AUG PMID[21534539]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23507152]
NPO40332 Salvia chamaedryoides Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[28186413]
NPO12148.2 Acer pictum subsp. okamotoanum Subspecies Sapindaceae Eukaryota n.a. n.a. n.a. PMID[9461665]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3291 Cynanchum auriculatum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18356 Stachys tuberifera Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18435 Tylophora atrofolliculata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17362 Alstonia yunnanensis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18356 Stachys tuberifera Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3291 Cynanchum auriculatum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17362 Alstonia yunnanensis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18435 Tylophora atrofolliculata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17362 Alstonia yunnanensis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3291 Cynanchum auriculatum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4984 Salvia cana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19638 Scutellaria albida Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4230 Protoparmeliopsis peltata Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12148.2 Acer pictum subsp. okamotoanum Subspecies Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19522 Arthropsis truncata Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17119 Dalea versicolor Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19311 Dasymaschalon blumei Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13832 Aspilia hispida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17783 Sideritis cystosiphon Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6098 Salvia officinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10852 Felimare midatlantica Species Chromodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17362 Alstonia yunnanensis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18055 Isodon adenolomus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16997 Talaromyces aculeatus Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3291 Cynanchum auriculatum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17643 Penicillium pedemontanum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16990 Verbesina virgata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17911 Blepharisma japonicum Species Blepharismidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18356 Stachys tuberifera Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15497 Caria ino Species Riodinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16567 Doriopsilla areolata Species Dendrodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2377 Cetraria ciliaris Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13414 Senecio fuertesii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18435 Tylophora atrofolliculata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19580 Chamaemelum fuscatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18606 Achyrocline bogotensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19777 Pholiota adiposa Species Strophariaceae 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 128.0 ug.mL-1 PMID[28186413]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MIC > 128.0 ug.mL-1 PMID[28186413]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 186000.0 nM PMID[28186413]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 93000.0 nM PMID[28186413]
NPT1531 Organism Enterococcus faecium Enterococcus faecium MIC = 186000.0 nM PMID[28186413]
NPT1531 Organism Enterococcus faecium Enterococcus faecium MIC = 93000.0 nM PMID[28186413]

☑ 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 NPC223573 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 NPC223573 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