Structure

Physi-Chem Properties

Molecular Weight:  186.13
Volume:  196.694
LogP:  0.377
LogD:  0.601
LogS:  -1.488
# Rotatable Bonds:  1
TPSA:  60.69
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.525
Synthetic Accessibility Score:  4.378
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.567
MDCK Permeability:  1.8609935068525374e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.916
Plasma Protein Binding (PPB):  24.721431732177734%
Volume Distribution (VD):  0.827
Pgp-substrate:  58.25993347167969%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.699
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.744
CYP2C9-inhibitor:  0.014
CYP2C9-substrate:  0.16
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.064
CYP3A4-inhibitor:  0.059
CYP3A4-substrate:  0.269

ADMET: Excretion

Clearance (CL):  4.615
Half-life (T1/2):  0.613

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.275
Drug-inuced Liver Injury (DILI):  0.043
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.057
Maximum Recommended Daily Dose:  0.447
Skin Sensitization:  0.256
Carcinogencity:  0.704
Eye Corrosion:  0.054
Eye Irritation:  0.981
Respiratory Toxicity:  0.159

Download Data

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

  Natural Product: NPC38419

Natural Product ID:  NPC38419
Common Name*:   VSZLGEHZLXBMON-VHSXEESVSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VSZLGEHZLXBMON-VHSXEESVSA-N
Standard InCHI:  InChI=1S/C10H18O3/c1-8(2,11)10(13)6-4-9(3,12)5-7-10/h4,6,11-13H,5,7H2,1-3H3/t9-,10+/m0/s1
SMILES:  CC(C)([C@]1(C=C[C@@](C)(CC1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001401] Menthane monoterpenoids

*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
NPO9771 Aka coralliphagum Species Niphatidae Eukaryota n.a. San Salvador in the Bahamas (12-26 m depth) 2001-MAR; 2003-JUL PMID[17309298]
NPO11402 Tithonia rotundifolia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9771 Aka coralliphagum Species Niphatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14637 Saussurea cordifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11402 Tithonia rotundifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2684 Cortinarius vinosipes Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14310 Tecoma heptaphylla Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13119 Hymenoxys microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4385 Aconitum zuccarini Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14222 Schefflera divaricata Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11166 Sclerodoris tanya n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11758 Parmelia pokornyi Species Parmeliaceae 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 NPC38419 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 NPC38419 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