Structure

Physi-Chem Properties

Molecular Weight:  378.15
Volume:  392.361
LogP:  6.123
LogD:  3.905
LogS:  -2.55
# Rotatable Bonds:  2
TPSA:  79.9
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.482
Synthetic Accessibility Score:  3.222
Fsp3:  0.261
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.768
MDCK Permeability:  1.6372900063288398e-05
Pgp-inhibitor:  0.839
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.144
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.03

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.013
Plasma Protein Binding (PPB):  90.0732192993164%
Volume Distribution (VD):  0.596
Pgp-substrate:  10.274707794189453%

ADMET: Metabolism

CYP1A2-inhibitor:  0.685
CYP1A2-substrate:  0.243
CYP2C19-inhibitor:  0.835
CYP2C19-substrate:  0.094
CYP2C9-inhibitor:  0.875
CYP2C9-substrate:  0.859
CYP2D6-inhibitor:  0.296
CYP2D6-substrate:  0.2
CYP3A4-inhibitor:  0.309
CYP3A4-substrate:  0.113

ADMET: Excretion

Clearance (CL):  2.058
Half-life (T1/2):  0.177

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.971
Drug-inuced Liver Injury (DILI):  0.982
AMES Toxicity:  0.313
Rat Oral Acute Toxicity:  0.985
Maximum Recommended Daily Dose:  0.556
Skin Sensitization:  0.695
Carcinogencity:  0.878
Eye Corrosion:  0.003
Eye Irritation:  0.063
Respiratory Toxicity:  0.748

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  Natural Product: NPC279242

Natural Product ID:  NPC279242
Common Name*:   YWHROXVOOAEFOY-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YWHROXVOOAEFOY-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C23H22O5/c1-12(2)8-9-15-20-14(10-11-23(3,4)28-20)19(26)17-18(25)13-6-5-7-16(24)21(13)27-22(15)17/h5-8,10-11,24,26H,9H2,1-4H3
SMILES:  CC(=CCc1c2c(C=CC(C)(C)O2)c(c2c(=O)c3cccc(c3oc12)O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   188341
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0002817] Dibenzopyrans
            • [CHEMONTID:0000200] Xanthenes
              • [CHEMONTID:0000204] Xanthones
                • [CHEMONTID:0003518] 4-prenylated xanthones

*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
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[10075773]
NPO9520 Cratoxylum sumatranum Species Hypericaceae Eukaryota n.a. twig n.a. PMID[11908969]
NPO9520 Cratoxylum sumatranum Species Hypericaceae Eukaryota n.a. stem n.a. PMID[11908969]
NPO9520 Cratoxylum sumatranum Species Hypericaceae Eukaryota n.a. leaf n.a. PMID[11908969]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. PMID[16933891]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18464091]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18558747]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota stem bark Pangradin village, Jasinga, West Java, Indonesia 2005-AUG PMID[19839614]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[20817450]
NPO16745 Scorzonera judaica Species Asteraceae Eukaryota n.a. tuberous root n.a. PMID[21650157]
NPO16745 Scorzonera judaica Species Asteraceae Eukaryota roots Daba desert reserve (50 km South of Amman), Jordan 2009-APR PMID[21650157]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. pericarp n.a. PMID[24555285]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[24717154]
NPO22497 Picrasma javanica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[26606140]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota fruit hulls Madras, Tamil Nadu, India 1993-MAR PMID[9213587]
NPO19227 Hippoglossus hippoglossus Species Pleuronectidae Eukaryota n.a. n.a. Database[FooDB]
NPO16038 Ribes rubrum Species Grossulariaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16038 Ribes rubrum Species Grossulariaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16038 Ribes rubrum Species Grossulariaceae Eukaryota Fruits n.a. Database[FooDB]
NPO19227 Hippoglossus hippoglossus Species Pleuronectidae Eukaryota n.a. n.a. Database[FooDB]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16038 Ribes rubrum Species Grossulariaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21218 Salvia aegyptiaca Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18995 Gaultheria itoana Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19359 Parmotrema delicatulum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9717 Wibelia divaricata Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10221 Streptomyces alboniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10056 Nicotiana sylvestris Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5221 Thamnolia subuliformis Species Icmadophilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16038 Ribes rubrum Species Grossulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7534 Leptogorgia sarmentosa Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3555 Cavernularia obesa Species Veretillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8560 Aplidium tabascum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19227 Hippoglossus hippoglossus Species Pleuronectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24931 Myelochroa aurulenta Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13263 Verbena brasiliensis Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9741 Actinopyga agassizi Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20085 Solenopsis xyloni Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22435 Abies lasiocarpa Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3707 Chromatium okenii Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8927 Poria selecta Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27924 Serpocaulon triseriale Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9520 Cratoxylum sumatranum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19501 Pseudosuberites hyalinus Species Suberitidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17438 Polygala virgata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22497 Picrasma javanica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14950 Ardisia polycephala Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6106 Hymeniacidon perlevis Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4064 Halimodendron halodendron Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19560 Populus italica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8354 Aster bellidiastrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21652 Decarya madagascariensis Species Didiereaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12600 Trametes cinnabarina Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18657 Galanthus gracilis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20963 Sarcopyramis bodinieri Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16745 Scorzonera judaica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11770 Amphicome emodi n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO21218 Salvia aegyptiaca Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22370 Baccharis calvescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3449 Lonicera hypoleuca Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18005 Artemisia leucodes Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25216 Senecio vellereus 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 NPC279242 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 NPC279242 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