Structure

Physi-Chem Properties

Molecular Weight:  232.15
Volume:  257.918
LogP:  2.642
LogD:  2.471
LogS:  -2.822
# Rotatable Bonds:  1
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.807
Synthetic Accessibility Score:  3.663
Fsp3:  0.533
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.529
MDCK Permeability:  1.9025015717488714e-05
Pgp-inhibitor:  0.031
Pgp-substrate:  0.114
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.982
30% Bioavailability (F30%):  0.967

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.853
Plasma Protein Binding (PPB):  93.01170349121094%
Volume Distribution (VD):  0.877
Pgp-substrate:  7.9554290771484375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.485
CYP1A2-substrate:  0.952
CYP2C19-inhibitor:  0.116
CYP2C19-substrate:  0.903
CYP2C9-inhibitor:  0.113
CYP2C9-substrate:  0.682
CYP2D6-inhibitor:  0.042
CYP2D6-substrate:  0.589
CYP3A4-inhibitor:  0.087
CYP3A4-substrate:  0.571

ADMET: Excretion

Clearance (CL):  3.203
Half-life (T1/2):  0.178

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.195
Drug-inuced Liver Injury (DILI):  0.179
AMES Toxicity:  0.091
Rat Oral Acute Toxicity:  0.115
Maximum Recommended Daily Dose:  0.493
Skin Sensitization:  0.098
Carcinogencity:  0.135
Eye Corrosion:  0.003
Eye Irritation:  0.171
Respiratory Toxicity:  0.344

Download Data

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

  Natural Product: NPC244619

Natural Product ID:  NPC244619
Common Name*:   PHOOTLGNMYEPGZ-JOYOIKCWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PHOOTLGNMYEPGZ-JOYOIKCWSA-N
Standard InCHI:  InChI=1S/C15H20O2/c1-8(2)11-6-13-10(4)14(16)7-12(13)9(3)5-15(11)17/h6,8-9,12H,5,7H2,1-4H3/t9-,12+/m0/s1
SMILES:  CC(C)C1=CC2=C(C)C(=O)C[C@@H]2[C@@H](C)CC1=O
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:0001550] Sesquiterpenoids
          • [CHEMONTID:0002874] Guaianes

*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
NPO25301 Angylocalyx pynaertii Species Fabaceae Eukaryota pods n.a. n.a. PMID[11858756]
NPO23049 Methanocaldococcus jannaschii Species Methanocaldococcaceae Archaea n.a. n.a. n.a. PMID[24977328]
NPO23049 Methanocaldococcus jannaschii Species Methanocaldococcaceae Archaea n.a. n.a. n.a. PMID[26100040]
NPO25301 Angylocalyx pynaertii Species Fabaceae Eukaryota seeds n.a. n.a. PMID[8229017]
NPO24584 Corydalis bungeana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24584 Corydalis bungeana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24584 Corydalis bungeana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24546 Diospyros siamang Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23560 Peridinium foliaceum Species Peridiniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25213 Physcia endococcina Species Physciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23521 Christiana africana Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24784 Forsythia ovata Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25301 Angylocalyx pynaertii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24751 Swartzia arborescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23644 Clitoria ternatea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24584 Corydalis bungeana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23049 Methanocaldococcus jannaschii Species Methanocaldococcaceae Archaea n.a. n.a. n.a. Database[UNPD]
NPO24467 Silene italica Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24625 Fannia canicularis Species Fanniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24913 Licania densiflora Species Chrysobalanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23602 Aspergillus parvulus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7271 Stachys affinis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24061 Zanthoxylum pistaciiflorum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23355 Astragalus arguricus Species Fabaceae 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 NPC244619 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 NPC244619 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