Structure

Physi-Chem Properties

Molecular Weight:  200.1
Volume:  196.928
LogP:  0.403
LogD:  0.581
LogS:  -0.321
# Rotatable Bonds:  0
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.543
Synthetic Accessibility Score:  4.21
Fsp3:  0.9
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:  -4.811
MDCK Permeability:  0.00012929047807119787
Pgp-inhibitor:  0.002
Pgp-substrate:  0.068
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.161

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.861
Plasma Protein Binding (PPB):  33.51732635498047%
Volume Distribution (VD):  0.88
Pgp-substrate:  71.87358856201172%

ADMET: Metabolism

CYP1A2-inhibitor:  0.023
CYP1A2-substrate:  0.174
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.79
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.154
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.156
CYP3A4-inhibitor:  0.026
CYP3A4-substrate:  0.299

ADMET: Excretion

Clearance (CL):  6.526
Half-life (T1/2):  0.736

ADMET: Toxicity

hERG Blockers:  0.023
Human Hepatotoxicity (H-HT):  0.32
Drug-inuced Liver Injury (DILI):  0.26
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.039
Maximum Recommended Daily Dose:  0.149
Skin Sensitization:  0.147
Carcinogencity:  0.506
Eye Corrosion:  0.022
Eye Irritation:  0.226
Respiratory Toxicity:  0.403

Download Data

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

  Natural Product: NPC235175

Natural Product ID:  NPC235175
Common Name*:   WMRLNPAAXAUOIO-BGJNVIQHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WMRLNPAAXAUOIO-BGJNVIQHSA-N
Standard InCHI:  InChI=1S/C10H16O4/c1-5-6-3-8(11)10(2,13)4-7(6)14-9(5)12/h5-8,11,13H,3-4H2,1-2H3/t5-,6-,7-,8+,10+/m1/s1
SMILES:  C[C@@H]1[C@H]2C[C@@H]([C@](C)(C[C@H]2OC1=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   14336593
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000301] Benzofurans

*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
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Anhui province, China DOI[10.1016/j.foodres.2020.109416]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Gansu province, China DOI[10.1016/j.foodres.2020.109416]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Henan province, China DOI[10.1016/j.foodres.2020.109416]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Shandong province, China DOI[10.1016/j.foodres.2020.109416]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Shanxi province, China DOI[10.1016/j.foodres.2020.109416]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. DOI[10.2174/092986712800229032]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. PMID[19402674]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[19721258]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[19772486]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Roots n.a. n.a. PMID[20806783]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[21782011]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[22190295]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. seed n.a. PMID[23497864]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[26838074]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[27313650]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[27429639]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Roots n.a. n.a. PMID[29741372]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds HeZe, ShanDong, China early autumn (from August to the beginning of September PMID[32545196]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Roots n.a. n.a. PMID[32951423]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Xinjiang,China PMID[33063333]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21458 Radix paeoniae rubra Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9798 Paeonia lactiflora Species Paeoniaceae 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 NPC235175 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 NPC235175 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