Structure

Physi-Chem Properties

Molecular Weight:  170.13
Volume:  193.824
LogP:  1.477
LogD:  0.711
LogS:  -1.047
# Rotatable Bonds:  5
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.616
Synthetic Accessibility Score:  3.74
Fsp3:  0.6
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:  -4.518
MDCK Permeability:  2.48542692133924e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.132
Plasma Protein Binding (PPB):  51.50579071044922%
Volume Distribution (VD):  0.99
Pgp-substrate:  54.064048767089844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.029
CYP1A2-substrate:  0.073
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.632
CYP2C9-inhibitor:  0.02
CYP2C9-substrate:  0.471
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.606
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.214

ADMET: Excretion

Clearance (CL):  6.968
Half-life (T1/2):  0.719

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.095
Drug-inuced Liver Injury (DILI):  0.141
AMES Toxicity:  0.218
Rat Oral Acute Toxicity:  0.586
Maximum Recommended Daily Dose:  0.875
Skin Sensitization:  0.882
Carcinogencity:  0.824
Eye Corrosion:  0.488
Eye Irritation:  0.956
Respiratory Toxicity:  0.937

Download Data

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

  Natural Product: NPC46752

Natural Product ID:  NPC46752
Common Name*:   RAMZBSSISHLRAN-SECBINFHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RAMZBSSISHLRAN-SECBINFHSA-N
Standard InCHI:  InChI=1S/C10H18O2/c1-5-8(2)6-7-9(11)10(3,4)12/h5,9,11-12H,1-2,6-7H2,3-4H3/t9-/m1/s1
SMILES:  C=CC(=C)CC[C@H](C(C)(C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11240729
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols

*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
NPO7979 Diospyros virginiana Species Ebenaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7979 Diospyros virginiana Species Ebenaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5194 Catha edulis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24028 Cissus adnata Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5194 Catha edulis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18002 Ipomoea obscura Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18586 Tamarix ramosissima Species Tamaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2255 Saturnia pavonia Species Saturniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16332 Liparis kumokiri Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15759 Boehmeria japonica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7402 Cornulaca monacantha Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7979 Diospyros virginiana Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5194 Catha edulis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13994 Piscidia mollis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16697 Solanum linearifolium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO483 Flacourtia inermis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2171 Acmella ciliata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6553 Pseudomonas savastanoi Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24028 Cissus adnata Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13033 Helichrysum setosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22565 Bidens graveolens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7256 Chresta sphaerocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5058 Synoicum macroglossum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18002 Ipomoea obscura Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16459 Lasthenia glabrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7068 Tanacetum annuum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14585 Iris xiphium Species Iridaceae 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 NPC46752 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 NPC46752 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