Structure

Physi-Chem Properties

Molecular Weight:  480.16
Volume:  441.172
LogP:  0.768
LogD:  0.122
LogS:  -3.452
# Rotatable Bonds:  7
TPSA:  164.37
# H-Bond Aceptor:  11
# H-Bond Donor:  5
# Rings:  8
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.306
Synthetic Accessibility Score:  6.16
Fsp3:  0.696
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -6.333
MDCK Permeability:  1.626021730771754e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.965
Human Intestinal Absorption (HIA):  0.861
20% Bioavailability (F20%):  0.756
30% Bioavailability (F30%):  0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.093
Plasma Protein Binding (PPB):  32.161163330078125%
Volume Distribution (VD):  0.65
Pgp-substrate:  38.01450729370117%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.991
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.628
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.034
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.083
CYP3A4-inhibitor:  0.095
CYP3A4-substrate:  0.127

ADMET: Excretion

Clearance (CL):  1.793
Half-life (T1/2):  0.824

ADMET: Toxicity

hERG Blockers:  0.099
Human Hepatotoxicity (H-HT):  0.06
Drug-inuced Liver Injury (DILI):  0.523
AMES Toxicity:  0.824
Rat Oral Acute Toxicity:  0.025
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.552
Carcinogencity:  0.894
Eye Corrosion:  0.003
Eye Irritation:  0.143
Respiratory Toxicity:  0.112

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  Natural Product: NPC56594

Natural Product ID:  NPC56594
Common Name*:   Paeoniflorin
IUPAC Name:   [(1R,2S,3R,5R,6R,8S)-6-hydroxy-8-methyl-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-9,10-dioxatetracyclo[4.3.1.02,5.03,8]decan-2-yl]methyl benzoate
Synonyms:  
Standard InCHIKey:  YKRGDOXKVOZESV-WRJNSLSBSA-N
Standard InCHI:  InChI=1S/C23H28O11/c1-20-9-22(29)13-7-23(20,32-18-16(27)15(26)14(25)12(8-24)31-18)21(13,19(33-20)34-22)10-30-17(28)11-5-3-2-4-6-11/h2-6,12-16,18-19,24-27,29H,7-10H2,1H3/t12-,13-,14-,15+,16-,18+,19-,20+,21+,22-,23+/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)CO)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   442534
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 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 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 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]
NPO15265 Paeonia rockii Species Paeoniaceae Eukaryota n.a. seed n.a. PMID[23497864]
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]
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 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]
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 20 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 30 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 Fruits Yangling, Shaanxi, China 60 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 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]
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]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15265 Paeonia rockii 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 NPC56594 n.a. Fruits 509 ± 25.08 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Fruits 328 ± 4.87 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Fruits 82.34 ± 1.36 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Fruits 30.24 ± 0.37 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Fruits 24.93 ± 1.09 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Fruits 6.94 ± 0.4 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Fruits 7.40 ± 0.21 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Fruits 3.37 ± 0.17 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Fruits 5.23 ± 0.04 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Fruits 10.16 ± 0.8 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 69.270 ± 0.261 n.a. n.a. μg/g PMID[32545196]
NPO15265 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 86.546 ± 0.077 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 61.463 ± 0.171 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 61.551 ± 0.260 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 23.049 ± 0.211 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 39.243 ± 1.839 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 64.616 +0.084 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 63.940 ± 0.160 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 35.220 ± 0.165 n.a. n.a. μg/g PMID[32545196]
NPO30287 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 60.259 ± 0.204 n.a. n.a. μg/g PMID[32545196]
NPO9798 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 41.255 ± 0.087 n.a. n.a. μg/g PMID[32545196]
NPO9798 NPC56594 Naturally dried; obtain oils by crushing seeds using screw press Seeds 77.222 ± 0.57 n.a. n.a. μg/g PMID[32545196]
NPO15265 NPC56594 n.a. Seeds 211 ± 17.41 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Seeds 1893 ± 31.52 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Seeds 1166 ± 65.93 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Seeds 392 ± 1.98 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Seeds 332 ± 12.9 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Seeds 251 ± 11.64 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Seeds 149 ± 0.27 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Seeds 84.61 ± 3.81 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Seeds 654 ± 16.64 n.a. n.a. mg/100g of DW PMID[33131958]
NPO15265 NPC56594 n.a. Seeds 480 ± 13.5 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 NPC56594 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 NPC56594 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