Structure

Physi-Chem Properties

Molecular Weight:  584.19
Volume:  551.932
LogP:  2.462
LogD:  1.562
LogS:  -3.837
# Rotatable Bonds:  10
TPSA:  170.44
# H-Bond Aceptor:  12
# H-Bond Donor:  4
# Rings:  9
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.318
Synthetic Accessibility Score:  6.087
Fsp3:  0.533
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.963
MDCK Permeability:  3.4853455872507766e-05
Pgp-inhibitor:  0.055
Pgp-substrate:  0.818
Human Intestinal Absorption (HIA):  0.451
20% Bioavailability (F20%):  0.875
30% Bioavailability (F30%):  0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.081
Plasma Protein Binding (PPB):  85.92364501953125%
Volume Distribution (VD):  0.916
Pgp-substrate:  6.285055160522461%

ADMET: Metabolism

CYP1A2-inhibitor:  0.024
CYP1A2-substrate:  0.971
CYP2C19-inhibitor:  0.038
CYP2C19-substrate:  0.226
CYP2C9-inhibitor:  0.201
CYP2C9-substrate:  0.038
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.07
CYP3A4-inhibitor:  0.566
CYP3A4-substrate:  0.304

ADMET: Excretion

Clearance (CL):  5.065
Half-life (T1/2):  0.753

ADMET: Toxicity

hERG Blockers:  0.259
Human Hepatotoxicity (H-HT):  0.031
Drug-inuced Liver Injury (DILI):  0.777
AMES Toxicity:  0.727
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.019
Skin Sensitization:  0.727
Carcinogencity:  0.662
Eye Corrosion:  0.003
Eye Irritation:  0.735
Respiratory Toxicity:  0.046

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  Natural Product: NPC190862

Natural Product ID:  NPC190862
Common Name*:   Benzoylpaeoniflorin
IUPAC Name:   [(2R,3S,4S,5R,6S)-6-[[(1R,2S,3R,5R,6R,8S)-2-(benzoyloxymethyl)-6-hydroxy-8-methyl-9,10-dioxatetracyclo[4.3.1.02,5.03,8]decan-3-yl]oxy]-3,4,5-trihydroxyoxan-2-yl]methyl benzoate
Synonyms:  
Standard InCHIKey:  LATYEZNGPQKAIK-HRCYFWENSA-N
Standard InCHI:  InChI=1S/C30H32O12/c1-27-14-29(36)19-12-30(27,28(19,26(41-27)42-29)15-38-24(35)17-10-6-3-7-11-17)40-25-22(33)21(32)20(31)18(39-25)13-37-23(34)16-8-4-2-5-9-16/h2-11,18-22,25-26,31-33,36H,12-15H2,1H3/t18-,19-,20-,21+,22-,25+,26-,27+,28+,29-,30+/m1/s1
SMILES:  C[C@]12C[C@@]3([C@@H]4C[C@]1([C@@]4([C@H](O2)O3)COC(=O)C5=CC=CC=C5)O[C@H]6[C@@H]([C@H]([C@@H]([C@H](O6)COC(=O)C7=CC=CC=C7)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   21631106
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides

*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]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota n.a. root n.a. PMID[21954959]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota roots Whitessence Srl, Viterbo, Italy 2005-OCT PMID[21954959]
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]
NPO15265 Paeonia rockii 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]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds DingXi, GanSu, China early autumn (from August to the beginning of September PMID[32545196]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds LanZhou, GanSu, China early autumn (from August to the beginning of September PMID[32545196]
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]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 20 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 80 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 30 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 90 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 40 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 50 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China Maturation PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 60 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 70 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 80 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 90 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China Maturation PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 10 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 20 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 30 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 40 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 50 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 60 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Fruits Yangling, Shaanxi, China 10 days after pollination PMID[33131958]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota Seeds Yangling, Shaanxi, China 70 days after pollination PMID[33131958]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
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]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
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
NPO15265 NPC190862 n.a. Fruits 27.50 ± 0.22 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Fruits 28.96 ± 2.43 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Fruits 8.99 ± 0.29 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Fruits 15.74 ± 0.45 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Fruits 2.93 ± 0.21 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Fruits 4.26 ± 0.26 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Fruits 1.21 ± 0.13 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Fruits 0.92 ± 0.06 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Fruits 1.06 ± 0.1f n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Fruits 0.28 ± 0.14 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.189 ± 0.005 n.a. n.a. μg/g PMID[32545196]
NPO15265 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.189 ± 0.000 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.251 ± 0.002 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.223 ± 0.002 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.267 ± 0.009 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.347 ± 0.001 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.258 ± 0.001 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.587 ± 0.001 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.303 ± 0.018 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.181 ± 0.012 n.a. n.a. μg/g PMID[32545196]
NPO9798 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.286 ± 0.000 n.a. n.a. μg/g PMID[32545196]
NPO9798 NPC190862 Naturally dried; obtain oils by crushing seeds using screw press Seeds 0.331 + 0.001 n.a. n.a. μg/g PMID[32545196]
NPO15265 NPC190862 n.a. Seeds 12.91 ± 1.09 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Seeds 10.03 ± 0.49 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Seeds 0.53 ± 0.11 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Seeds 0.34 ± 0.03 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Seeds 0.21 ± 0.04 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Seeds 0.29 ± 0.08 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Seeds 0.28 ± 0.03 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Seeds 0.15 ± 0.02 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Seeds 0.58 ± 0.08 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC190862 n.a. Seeds 0.30 ± 0.05 n.a. n.a. mg/100g of DW PMID[33131958]

☑ 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 NPC190862 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 NPC190862 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