Structure

Physi-Chem Properties

Molecular Weight:  316.09
Volume:  311.205
LogP:  2.481
LogD:  2.164
LogS:  -3.863
# Rotatable Bonds:  5
TPSA:  78.88
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.673
Synthetic Accessibility Score:  2.788
Fsp3:  0.294
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.683
MDCK Permeability:  2.7909169148188084e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.036
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.013
Plasma Protein Binding (PPB):  86.53194427490234%
Volume Distribution (VD):  0.915
Pgp-substrate:  12.012953758239746%

ADMET: Metabolism

CYP1A2-inhibitor:  0.971
CYP1A2-substrate:  0.943
CYP2C19-inhibitor:  0.768
CYP2C19-substrate:  0.289
CYP2C9-inhibitor:  0.805
CYP2C9-substrate:  0.577
CYP2D6-inhibitor:  0.603
CYP2D6-substrate:  0.508
CYP3A4-inhibitor:  0.675
CYP3A4-substrate:  0.351

ADMET: Excretion

Clearance (CL):  13.46
Half-life (T1/2):  0.821

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.848
Drug-inuced Liver Injury (DILI):  0.978
AMES Toxicity:  0.319
Rat Oral Acute Toxicity:  0.718
Maximum Recommended Daily Dose:  0.036
Skin Sensitization:  0.169
Carcinogencity:  0.821
Eye Corrosion:  0.003
Eye Irritation:  0.049
Respiratory Toxicity:  0.414

Download Data

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

  Natural Product: NPC3823

Natural Product ID:  NPC3823
Common Name*:   ZJSIKVDEOWWVEH-ZIAGYGMSSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZJSIKVDEOWWVEH-ZIAGYGMSSA-N
Standard InCHI:  InChI=1S/C15H24/c1-11-7-8-13-12(2)6-5-9-15(3,4)14(13)10-11/h10,13-14H,2,5-9H2,1,3-4H3/t13-,14-/m1/s1
SMILES:  CC1=C[C@@H]2[C@H](CC1)C(=C)CCCC2(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11769623
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0003545] Himachalane and lippifoliane sesquiterpenoids

*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
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(98)00208-8]
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[12951092]
NPO6609 Trigonostemon heterophyllus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[22122667]
NPO6609 Trigonostemon heterophyllus Species Euphorbiaceae Eukaryota n.a. twig n.a. PMID[22122667]
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26575 Scapania undulata Species Scapaniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26575 Scapania undulata Species Scapaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO937 Limnodynastes terraereginae Species Myobatrachidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26818 Euphorbia kaleniczenkii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26178 Guarea glabra Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26390 Triphasia trifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26519 Acanthodoris nanaimoensis Species Onchidorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26872 Piper betle Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25939 Lupinus macounii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26360 Methysticodendron amesianum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO4408 Alstonia rostrata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6609 Trigonostemon heterophyllus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10837 Matthiola incana Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25961 Liatris graminifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26275 Dactynotus rudbeckiae n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7055 Lychnophora hakeaefolia Species Asteraceae 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 NPC3823 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 NPC3823 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