Structure

Physi-Chem Properties

Molecular Weight:  334.21
Volume:  356.058
LogP:  3.786
LogD:  3.012
LogS:  -3.764
# Rotatable Bonds:  0
TPSA:  59.06
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.318
Synthetic Accessibility Score:  5.673
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.578
MDCK Permeability:  3.410790304769762e-05
Pgp-inhibitor:  0.8
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.085
30% Bioavailability (F30%):  0.485

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.074
Plasma Protein Binding (PPB):  92.10103607177734%
Volume Distribution (VD):  1.53
Pgp-substrate:  6.665266513824463%

ADMET: Metabolism

CYP1A2-inhibitor:  0.046
CYP1A2-substrate:  0.156
CYP2C19-inhibitor:  0.159
CYP2C19-substrate:  0.633
CYP2C9-inhibitor:  0.247
CYP2C9-substrate:  0.071
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.117
CYP3A4-inhibitor:  0.615
CYP3A4-substrate:  0.267

ADMET: Excretion

Clearance (CL):  8.823
Half-life (T1/2):  0.247

ADMET: Toxicity

hERG Blockers:  0.058
Human Hepatotoxicity (H-HT):  0.22
Drug-inuced Liver Injury (DILI):  0.318
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.057
Maximum Recommended Daily Dose:  0.921
Skin Sensitization:  0.95
Carcinogencity:  0.258
Eye Corrosion:  0.803
Eye Irritation:  0.697
Respiratory Toxicity:  0.963

Download Data

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

  Natural Product: NPC96240

Natural Product ID:  NPC96240
Common Name*:   YKKJETNBRNDYKN-JZZWRREUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YKKJETNBRNDYKN-JZZWRREUSA-N
Standard InCHI:  InChI=1S/C20H30O4/c1-13-6-5-10-19(3,22)17-12-15(14(2)18(21)23-17)9-11-20(4)16(24-20)8-7-13/h6,15-17,22H,2,5,7-12H2,1,3-4H3/b13-6+/t15-,16+,17-,19+,20+/m1/s1
SMILES:  C/C/1=CCC[C@@](C)([C@H]2C[C@@H](CC[C@@]3(C)[C@H](CC1)O3)C(=C)C(=O)O2)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5458571
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000147] Macrolides and analogues

*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
NPO3286 Erythrina americana Species Fabaceae Eukaryota Flowers Tantempango, Hidalgo, Mexico 2019-May DOI[10.1007/s11130-020-00822-2]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota n.a. seed n.a. DOI[10.1016/0031-9422(96)00258-0]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota n.a. fruit n.a. DOI[10.1016/S1383-5769(99)00023-9]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[10086989]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[1512598]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota Seeds n.a. n.a. PMID[15165151]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota fruit Indonesia n.a. PMID[17896817]
NPO7475 Sinularia querciformis Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[18831569]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota n.a. Vietnam n.a. PMID[19026551]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota seeds n.a. n.a. PMID[20050684]
NPO10949 Riccardia multifida Species Aneuraceae Eukaryota n.a. n.a. n.a. PMID[21625478]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota Seeds n.a. n.a. PMID[22506620]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[6481366]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[7561896]
NPO3371 Podocarpus nubigenus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3286 Erythrina americana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3371 Podocarpus nubigenus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3286 Erythrina americana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3371 Podocarpus nubigenus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3286 Erythrina americana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14948 Brucea javanica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5448 Wattakaka volubilis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3048 Laportea moroides Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7475 Sinularia querciformis Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3286 Erythrina americana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11440 Dictyota menstrualis Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3371 Podocarpus nubigenus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9011 Anaptychia neoleucomelaena Species Physciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7724 Heterobasidion annosum Species Bondarzewiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10949 Riccardia multifida Species Aneuraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4491 Aplophyllum cappadocicum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10200 Pourouma cecropiifolia Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6712 Artocarpus scortechinii Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2735 Orthodon hirtus Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO232 Cayaponia racemosa Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14948 Brucea javanica Species Simaroubaceae 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 NPC96240 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 NPC96240 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