Structure

Physi-Chem Properties

Molecular Weight:  264.14
Volume:  275.498
LogP:  2.483
LogD:  2.224
LogS:  -2.768
# Rotatable Bonds:  3
TPSA:  47.92
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.911
Synthetic Accessibility Score:  3.376
Fsp3:  0.467
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:  -4.616
MDCK Permeability:  1.8198816178482957e-05
Pgp-inhibitor:  0.873
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.036

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.874
Plasma Protein Binding (PPB):  84.26485443115234%
Volume Distribution (VD):  1.717
Pgp-substrate:  15.266990661621094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.797
CYP1A2-substrate:  0.81
CYP2C19-inhibitor:  0.179
CYP2C19-substrate:  0.88
CYP2C9-inhibitor:  0.093
CYP2C9-substrate:  0.828
CYP2D6-inhibitor:  0.392
CYP2D6-substrate:  0.297
CYP3A4-inhibitor:  0.169
CYP3A4-substrate:  0.745

ADMET: Excretion

Clearance (CL):  4.252
Half-life (T1/2):  0.31

ADMET: Toxicity

hERG Blockers:  0.042
Human Hepatotoxicity (H-HT):  0.681
Drug-inuced Liver Injury (DILI):  0.013
AMES Toxicity:  0.044
Rat Oral Acute Toxicity:  0.839
Maximum Recommended Daily Dose:  0.907
Skin Sensitization:  0.13
Carcinogencity:  0.381
Eye Corrosion:  0.003
Eye Irritation:  0.109
Respiratory Toxicity:  0.481

Download Data

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

  Natural Product: NPC233196

Natural Product ID:  NPC233196
Common Name*:   WLLPYKPZYOAPQI-SECBINFHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WLLPYKPZYOAPQI-SECBINFHSA-N
Standard InCHI:  InChI=1S/C15H20O4/c1-9(16)11-8-10-6-7-15(2,3)19-12(10)14(18-5)13(11)17-4/h6-9,16H,1-5H3/t9-/m1/s1
SMILES:  C[C@H](c1cc2C=CC(C)(C)Oc2c(c1OC)OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   100945948
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0003522] 2,2-dimethyl-1-benzopyrans

*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
NPO2257 Oceanapia phillipensis Species Phloeodictyidae Eukaryota n.a. n.a. n.a. PMID[10654417]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[15516765]
NPO10996 Ferula assa-foetida Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[19691312]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[20973550]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[23700450]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. leaf n.a. PMID[23849114]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[24310066]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. seed n.a. PMID[25433632]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. seed n.a. PMID[26860358]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. PMID[31861466]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Petiole n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Protoplast n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8981 Senecio integerrimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5511 Populus tremula Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. seed n.a. Database[MetaboLights]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO5511 Populus tremula Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8981 Senecio integerrimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO592 Chroogomphus rutilus Species Gomphidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5890 Astragalus inopinatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10073 Clusia torresii Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1408 Cirsium helenioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2257 Oceanapia phillipensis Species Phloeodictyidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5511 Populus tremula Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14887 Handroanthus guayacan Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1638 Ulmus laciniata Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10996 Ferula assa-foetida Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2499 Celmisia petriei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8981 Senecio integerrimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11235 Asplenium nidus Species Aspleniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14797 Orthosiphon aristatus Species Lamiaceae 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 NPC233196 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 NPC233196 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