Structure

Physi-Chem Properties

Molecular Weight:  309.17
Volume:  338.929
LogP:  5.959
LogD:  3.95
LogS:  -3.785
# Rotatable Bonds:  5
TPSA:  56.25
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.441
Synthetic Accessibility Score:  2.759
Fsp3:  0.3
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.011
MDCK Permeability:  1.7647458662395366e-05
Pgp-inhibitor:  0.025
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.114
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.173
Plasma Protein Binding (PPB):  99.33882141113281%
Volume Distribution (VD):  3.304
Pgp-substrate:  1.3895883560180664%

ADMET: Metabolism

CYP1A2-inhibitor:  0.979
CYP1A2-substrate:  0.691
CYP2C19-inhibitor:  0.86
CYP2C19-substrate:  0.086
CYP2C9-inhibitor:  0.705
CYP2C9-substrate:  0.855
CYP2D6-inhibitor:  0.758
CYP2D6-substrate:  0.882
CYP3A4-inhibitor:  0.218
CYP3A4-substrate:  0.114

ADMET: Excretion

Clearance (CL):  5.443
Half-life (T1/2):  0.436

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.046
Drug-inuced Liver Injury (DILI):  0.087
AMES Toxicity:  0.466
Rat Oral Acute Toxicity:  0.167
Maximum Recommended Daily Dose:  0.393
Skin Sensitization:  0.951
Carcinogencity:  0.886
Eye Corrosion:  0.035
Eye Irritation:  0.967
Respiratory Toxicity:  0.931

Download Data

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

  Natural Product: NPC258033

Natural Product ID:  NPC258033
Common Name*:   XFGOIZUEQXLEAH-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XFGOIZUEQXLEAH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C20H23NO2/c1-3-4-5-6-7-10-14-13(2)19(22)20(23)17-15-11-8-9-12-16(15)21-18(14)17/h8-9,11-12,21H,3-7,10H2,1-2H3
SMILES:  CCCCCCCC1=C(C)C(=O)C(=O)c2c3ccccc3[nH]c12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10335508
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000211] Indoles and derivatives
        • [CHEMONTID:0000210] Carbazoles

*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
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[1002/hlca.19760590517]
NPO40704 Streptomyces sp. RKND-216 + Alteromonas sp. RKMC-009 Species Co-culture n.a. n.a. n.a. n.a. n.a. PMID[32869646]
NPO40705 Streptomyces sp. RKND-216 + Mycobacterium smegmatis ATCC 120515 Species Co-culture n.a. n.a. n.a. n.a. n.a. PMID[32869646]
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[931752]
NPO25885 Drupella fragum Species Muricidae Eukaryota n.a. n.a. n.a. PMID[9722496]
NPO25782 Crotalaria trifoliastrum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9784166]
NPO26911 Mesua thwaitesii Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25912 Leontice smirnowii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26769 Montanoa tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26911 Mesua thwaitesii Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25912 Leontice smirnowii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26616 Piper novae-hollandiae Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26420 Swertia perennis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28906 Cossus cossus Species Cossidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3732 Entoleuca mammata Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4085 Cephalaria lycica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26891 Pinus nigra Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25861 Helminthosporium catenarium Species Massarinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26310 Panax ricinifolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27039 Poterium polygamum Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26198 Halimeda scabra Species Halimedaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26998 Goniotrichum elegans n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26911 Mesua thwaitesii Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25885 Drupella fragum Species Muricidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26796 Tropaeolum peregrinum Species Tropaeolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13835 Aristolochia serpentaria Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19417 Cochliobolus pallescens Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11483 Adenocarpus decorticans Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26276 Haplopappus taeda Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26769 Montanoa tomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25782 Crotalaria trifoliastrum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25912 Leontice smirnowii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26713 Lasius umbratus Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26600 Glottiphyllum longum Species Aizoaceae 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
NPT83 Cell Line MCF7 Homo sapiens IC50 = 3070.0 nM PMID[32869646]
NPT2 Others Unspecified IC50 = 3670.0 nM PMID[32869646]

☑ 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 NPC258033 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 NPC258033 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