Structure

Physi-Chem Properties

Molecular Weight:  314.19
Volume:  336.075
LogP:  4.109
LogD:  3.57
LogS:  -3.19
# Rotatable Bonds:  0
TPSA:  50.44
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.758
Synthetic Accessibility Score:  4.49
Fsp3:  0.65
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:  -4.871
MDCK Permeability:  2.8218744773766957e-05
Pgp-inhibitor:  0.627
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.191

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.095
Plasma Protein Binding (PPB):  96.24535369873047%
Volume Distribution (VD):  1.376
Pgp-substrate:  3.504133939743042%

ADMET: Metabolism

CYP1A2-inhibitor:  0.226
CYP1A2-substrate:  0.741
CYP2C19-inhibitor:  0.089
CYP2C19-substrate:  0.825
CYP2C9-inhibitor:  0.31
CYP2C9-substrate:  0.743
CYP2D6-inhibitor:  0.03
CYP2D6-substrate:  0.697
CYP3A4-inhibitor:  0.111
CYP3A4-substrate:  0.3

ADMET: Excretion

Clearance (CL):  18.016
Half-life (T1/2):  0.481

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.722
Drug-inuced Liver Injury (DILI):  0.223
AMES Toxicity:  0.033
Rat Oral Acute Toxicity:  0.818
Maximum Recommended Daily Dose:  0.847
Skin Sensitization:  0.441
Carcinogencity:  0.942
Eye Corrosion:  0.01
Eye Irritation:  0.265
Respiratory Toxicity:  0.983

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC34555

Natural Product ID:  NPC34555
Common Name*:   JFINBCWMRIJTDN-NLDJYOPPSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JFINBCWMRIJTDN-NLDJYOPPSA-N
Standard InCHI:  InChI=1S/C20H26O3/c1-11-13-9-12-5-6-16-19(2,3)17(21)7-8-20(16,4)14(12)10-15(13)23-18(11)22/h9,14-16H,5-8,10H2,1-4H3/t14-,15-,16-,20+/m1/s1
SMILES:  CC1=C2C=C3CC[C@@H]4C(C)(C)C(=O)CC[C@@]4(C)[C@@H]3C[C@H]2OC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11565893
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001538] Diterpene lactones

*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
NPO26629 Caesalpinia pulcherrima Species Fabaceae Eukaryota n.a. stem n.a. DOI[10.1021/np0201523]
NPO26629 Caesalpinia pulcherrima Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[12193012]
NPO26661 Heimia salicifolia Species Lythraceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO25837 Euphorbia micractina Species Euphorbiaceae Eukaryota Roots Zhang County, Gansu Province, China 2002-Sep PMID[19702283]
NPO25837 Euphorbia micractina Species Euphorbiaceae Eukaryota n.a. root n.a. PMID[21534583]
NPO25837 Euphorbia micractina Species Euphorbiaceae Eukaryota Roots n.a. n.a. PMID[23691978]
NPO40127 Euphorbia soongarica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[28590124]
NPO40126 Euphorbia pedroi Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[30199257]
NPO26629 Caesalpinia pulcherrima Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[3783154]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8770 Euphorbia wallichii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26629 Caesalpinia pulcherrima Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26629 Caesalpinia pulcherrima Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8770 Euphorbia wallichii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18641 Radix euphorbiae pekinensis Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26172 Dryopteris sacrosancta Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12190 Carduus acanthoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26411 Stemphylium radicinum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26661 Heimia salicifolia Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26888 Narcissus asturiensis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26568 Rubus koehneanus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4283 Tripteris vaillantii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25876 Chromodoris inornata Species Chromodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26172 Dryopteris sacrosancta Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25837 Euphorbia micractina Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26190 Aspergillus wentii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29041 Scutellaria orientalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26215 Eleusine indica Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21065 Euphorbia calyptrata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26433 Conus marmoreus Species Conidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1891 Chorilaena quercifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21665.1 Mycobacterium avium subsp. paratuberculosis Subspecies Mycobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8770 Euphorbia wallichii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26629 Caesalpinia pulcherrima Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26906 Astragalus interpositus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12190 Carduus acanthoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8081 Crataegus flava Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5402 Hypogymnia billardieri Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26839 Microlepia speluncae Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16779.1 Amaranthus hybridus subsp. cruentus Subspecies Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26931 Dolichothele uberiformis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO21295 Botryotrichum piluliferum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26383 Lemna trisulca Species Araceae 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
NPT91 Cell Line KB Homo sapiens IC50 = 22440.0 nM PMID[28590124]
NPT886 Cell Line NIH3T3 Mus musculus IC50 > 10000.0 nM PMID[30199257]
NPT407 Cell Line COLO 205 Homo sapiens IC50 > 10000.0 nM PMID[30199257]
NPT2641 Cell Line COLO 320 Homo sapiens IC50 > 10000.0 nM PMID[30199257]
NPT1864 Cell Line L5178Y Mus musculus IC50 > 10000.0 nM PMID[30199257]
NPT171 Cell Line MRC5 Homo sapiens IC50 > 10000.0 nM PMID[30199257]
NPT2 Others Unspecified IC50 > 30000.0 nM PMID[28590124]
NPT2 Others Unspecified Ratio = 0.45 n.a. PMID[28590124]
NPT668 Individual Protein P-glycoprotein 1 Homo sapiens Ratio = 1.84 n.a. PMID[30199257]
NPT668 Individual Protein P-glycoprotein 1 Homo sapiens Ratio = 10.23 n.a. PMID[30199257]
NPT668 Individual Protein P-glycoprotein 1 Homo sapiens Ratio = 0.44 n.a. PMID[30199257]
NPT668 Individual Protein P-glycoprotein 1 Homo sapiens Ratio = 0.98 n.a. PMID[30199257]

☑ 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 NPC34555 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 NPC34555 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