Structure

Physi-Chem Properties

Molecular Weight:  272.25
Volume:  329.454
LogP:  6.42
LogD:  4.667
LogS:  -5.597
# Rotatable Bonds:  3
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.417
Synthetic Accessibility Score:  4.131
Fsp3:  0.7
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.55
MDCK Permeability:  1.0409624337626155e-05
Pgp-inhibitor:  0.884
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.919
30% Bioavailability (F30%):  0.103

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.199
Plasma Protein Binding (PPB):  84.98526763916016%
Volume Distribution (VD):  2.281
Pgp-substrate:  11.499785423278809%

ADMET: Metabolism

CYP1A2-inhibitor:  0.224
CYP1A2-substrate:  0.247
CYP2C19-inhibitor:  0.309
CYP2C19-substrate:  0.926
CYP2C9-inhibitor:  0.358
CYP2C9-substrate:  0.434
CYP2D6-inhibitor:  0.195
CYP2D6-substrate:  0.886
CYP3A4-inhibitor:  0.571
CYP3A4-substrate:  0.424

ADMET: Excretion

Clearance (CL):  9.792
Half-life (T1/2):  0.058

ADMET: Toxicity

hERG Blockers:  0.037
Human Hepatotoxicity (H-HT):  0.559
Drug-inuced Liver Injury (DILI):  0.073
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.325
Maximum Recommended Daily Dose:  0.901
Skin Sensitization:  0.924
Carcinogencity:  0.687
Eye Corrosion:  0.961
Eye Irritation:  0.91
Respiratory Toxicity:  0.967

Download Data

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

  Natural Product: NPC76708

Natural Product ID:  NPC76708
Common Name*:   VJVMMXUPZGOBSN-CMKODMSKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VJVMMXUPZGOBSN-CMKODMSKSA-N
Standard InCHI:  InChI=1S/C20H32/c1-7-15(2)9-11-17-16(3)10-12-18-19(4,5)13-8-14-20(17,18)6/h7,9,17-18H,1,3,8,10-14H2,2,4-6H3/t17-,18-,20+/m0/s1
SMILES:  C=CC(=CC[C@H]1C(=C)CC[C@H]2C(C)(C)CCC[C@]12C)C
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:0001551] Diterpenoids

*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
NPO3031 Sabal causiarum Species Arecaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11508 Polygala reinii Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11975 Antillogorgia elisabethae Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1402 Adenocarpus foliolosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14173 Ipomoea reptans Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7550 Chromolaena arnottiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11508 Polygala reinii Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13484 Vidalia volubilis Species Tephritidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29061 Anthoxanthum nitens Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6564 Betula exilis Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22285 Clethra macrophylla Species Clethraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13183 Cereus dumortieri Species Sagartiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3031 Sabal causiarum Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19055 Plenodomus tracheiphilus Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10309 Ichthyothere terminalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14374 Retama duriaei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11036 Piper taboganum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14581 Rubia schumanniana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13884 Microglossa pyrrhopappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10163 Oreoherzogia fallax Species Rhamnaceae 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 NPC76708 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 NPC76708 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