Structure

Physi-Chem Properties

Molecular Weight:  624.17
Volume:  569.614
LogP:  0.732
LogD:  0.098
LogS:  -4.354
# Rotatable Bonds:  7
TPSA:  258.43
# H-Bond Aceptor:  16
# H-Bond Donor:  9
# Rings:  5
# Heavy Atoms:  16

MedChem Properties

QED Drug-Likeness Score:  0.137
Synthetic Accessibility Score:  4.751
Fsp3:  0.464
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.4
MDCK Permeability:  2.0682806280092336e-05
Pgp-inhibitor:  0.045
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.82
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.061
Plasma Protein Binding (PPB):  84.49930572509766%
Volume Distribution (VD):  0.667
Pgp-substrate:  16.708370208740234%

ADMET: Metabolism

CYP1A2-inhibitor:  0.087
CYP1A2-substrate:  0.079
CYP2C19-inhibitor:  0.034
CYP2C19-substrate:  0.057
CYP2C9-inhibitor:  0.018
CYP2C9-substrate:  0.276
CYP2D6-inhibitor:  0.071
CYP2D6-substrate:  0.153
CYP3A4-inhibitor:  0.04
CYP3A4-substrate:  0.005

ADMET: Excretion

Clearance (CL):  1.524
Half-life (T1/2):  0.688

ADMET: Toxicity

hERG Blockers:  0.133
Human Hepatotoxicity (H-HT):  0.075
Drug-inuced Liver Injury (DILI):  0.98
AMES Toxicity:  0.85
Rat Oral Acute Toxicity:  0.029
Maximum Recommended Daily Dose:  0.009
Skin Sensitization:  0.784
Carcinogencity:  0.089
Eye Corrosion:  0.003
Eye Irritation:  0.293
Respiratory Toxicity:  0.027

Download Data

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

  Natural Product: NPC41436

Natural Product ID:  NPC41436
Common Name*:   ZDLUERJVCJYBIT-IIRAHQKESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZDLUERJVCJYBIT-IIRAHQKESA-N
Standard InCHI:  InChI=1S/C20H28O5/c1-11-12-4-5-13-19(10-22)7-3-6-18(2,9-21)14(19)8-15(23)20(13,16(11)24)17(12)25/h9,12-15,17,22-23,25H,1,3-8,10H2,2H3/t12-,13-,14+,15+,17+,18+,19+,20-/m0/s1
SMILES:  C=C1[C@@H]2CC[C@H]3[C@@]4(CCC[C@](C)(C=O)[C@H]4C[C@H]([C@@]3(C1=O)[C@@H]2O)O)CO
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
          • [CHEMONTID:0003782] Kaurane 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
NPO1238 Gentiana brachyphylla Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)94333-4]
NPO15395 Euphorbia portlandica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[16792416]
NPO3902 Aglaia edulis Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[17190457]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. heartwood n.a. PMID[21488654]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota Heartwood India n.a. PMID[21488654]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota heartwood n.a. n.a. PMID[21784631]
NPO1238 Gentiana brachyphylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8694 Picrasma crenata Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15395 Euphorbia portlandica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1238 Gentiana brachyphylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18360 Isodon weisiensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8694 Picrasma crenata Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3902 Aglaia edulis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15395 Euphorbia portlandica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1238 Gentiana brachyphylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21411 Santolina magonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1238 Gentiana brachyphylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO688 Scorzonera cretica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7927 Stephania lincangensis Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8694 Picrasma crenata Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3766 Dodartia orientalis Species Phrymaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18360 Isodon weisiensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7594 Muricea californica Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6120 Attalea funifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3038 Veronica linariifolia Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5138 Colebrookea oppositifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24506 Prionoxystus robiniae Species Cossidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3902 Aglaia edulis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4558 Polysaccum crassipes n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO8191 Lecanora epanora Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11368 Leontodon tuberosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO265 Helminthosporium zizaniae Species Massarinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15395 Euphorbia portlandica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1531 Chlorella sorokiniana Species Chlorellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4800 Cyrtocymura cincta 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 NPC41436 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 NPC41436 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