Structure

Physi-Chem Properties

Molecular Weight:  276.14
Volume:  290.158
LogP:  4.652
LogD:  3.679
LogS:  -4.192
# Rotatable Bonds:  6
TPSA:  59.67
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.818
Synthetic Accessibility Score:  2.274
Fsp3:  0.438
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:  -4.786
MDCK Permeability:  2.4112339815474115e-05
Pgp-inhibitor:  0.05
Pgp-substrate:  0.16
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.946
30% Bioavailability (F30%):  0.97

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.073
Plasma Protein Binding (PPB):  97.9506607055664%
Volume Distribution (VD):  0.775
Pgp-substrate:  3.2990634441375732%

ADMET: Metabolism

CYP1A2-inhibitor:  0.981
CYP1A2-substrate:  0.935
CYP2C19-inhibitor:  0.945
CYP2C19-substrate:  0.365
CYP2C9-inhibitor:  0.864
CYP2C9-substrate:  0.955
CYP2D6-inhibitor:  0.742
CYP2D6-substrate:  0.917
CYP3A4-inhibitor:  0.518
CYP3A4-substrate:  0.154

ADMET: Excretion

Clearance (CL):  4.007
Half-life (T1/2):  0.378

ADMET: Toxicity

hERG Blockers:  0.037
Human Hepatotoxicity (H-HT):  0.087
Drug-inuced Liver Injury (DILI):  0.592
AMES Toxicity:  0.66
Rat Oral Acute Toxicity:  0.088
Maximum Recommended Daily Dose:  0.601
Skin Sensitization:  0.923
Carcinogencity:  0.08
Eye Corrosion:  0.106
Eye Irritation:  0.969
Respiratory Toxicity:  0.654

Download Data

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

  Natural Product: NPC306935

Natural Product ID:  NPC306935
Common Name*:   JNHVWACAXZPGJO-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JNHVWACAXZPGJO-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H20O4/c1-3-4-5-6-7-11-8-13(17)16-14(18)9-12(19-2)10-15(16)20-11/h8-10,18H,3-7H2,1-2H3
SMILES:  CCCCCCc1cc(=O)c2c(cc(cc2o1)OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0000144] Chromones

*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]
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]
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]

☑ 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 NPC306935 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 NPC306935 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