Structure

Physi-Chem Properties

Molecular Weight:  896.51
Volume:  888.387
LogP:  3.956
LogD:  3.358
LogS:  -3.941
# Rotatable Bonds:  7
TPSA:  254.52
# H-Bond Aceptor:  16
# H-Bond Donor:  9
# Rings:  8
# Heavy Atoms:  16

MedChem Properties

QED Drug-Likeness Score:  0.131
Synthetic Accessibility Score:  6.267
Fsp3:  0.936
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.626
MDCK Permeability:  2.3896118364064023e-05
Pgp-inhibitor:  0.976
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.752
20% Bioavailability (F20%):  0.027
30% Bioavailability (F30%):  0.97

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.046
Plasma Protein Binding (PPB):  85.4168930053711%
Volume Distribution (VD):  0.127
Pgp-substrate:  13.398833274841309%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.137
CYP2C19-inhibitor:  0.002
CYP2C19-substrate:  0.202
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.024
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.074
CYP3A4-inhibitor:  0.035
CYP3A4-substrate:  0.013

ADMET: Excretion

Clearance (CL):  0.51
Half-life (T1/2):  0.649

ADMET: Toxicity

hERG Blockers:  0.075
Human Hepatotoxicity (H-HT):  0.177
Drug-inuced Liver Injury (DILI):  0.028
AMES Toxicity:  0.077
Rat Oral Acute Toxicity:  0.192
Maximum Recommended Daily Dose:  0.953
Skin Sensitization:  0.133
Carcinogencity:  0.019
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.964

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

  Natural Product: NPC252750

Natural Product ID:  NPC252750
Common Name*:   AVJNWIDNAJCPRK-USYDSXQJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  AVJNWIDNAJCPRK-USYDSXQJSA-N
Standard InCHI:  InChI=1S/C47H76O16/c1-21-29(50)31(52)34(55)39(59-21)62-36-30(51)24(48)20-58-40(36)63-37-33(54)32(53)35(38(56)57)61-41(37)60-28-13-14-45(7)25(43(28,4)5)12-15-47(9)26(45)11-10-22-23-18-42(2,3)19-27(49)44(23,6)16-17-46(22,47)8/h10,21,23-37,39-41,48-55H,11-20H2,1-9H3,(H,56,57)/t21-,23-,24-,25-,26+,27+,28-,29-,30-,31+,32-,33-,34+,35-,36+,37+,39-,40-,41+,44+,45-,46+,47+/m0/s1
SMILES:  C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@H](CO[C@H]1O[C@@H]1[C@H]([C@@H]([C@@H](C(=O)O)O[C@H]1O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC=C2[C@@H]4CC(C)(C)C[C@H]([C@]4(C)CC[C@@]32C)O)C1(C)C)O)O)O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   100945993
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene saponins

*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
NPO25932 Delphinium barbeyi Species Ranunculaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf00025a020]
NPO9446 Asterias rathbuni Species Asteriidae Eukaryota n.a. n.a. n.a. PMID[11473430]
NPO25932 Delphinium barbeyi Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8707.1 Pueraria montana var. lobata Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8707.2 Pueraria montana var. thomsonii Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25932 Delphinium barbeyi Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8707.2 Pueraria montana var. thomsonii Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8707.1 Pueraria montana var. lobata Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13715 Bertya dimerostigma Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5081 Amorphinopsis foetida Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6243 Fomes fastuosus Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9446 Asterias rathbuni Species Asteriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5479 Astragalus wiedemannianus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25932 Delphinium barbeyi Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8707.2 Pueraria montana var. thomsonii Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8707.1 Pueraria montana var. lobata Varieties Fabaceae 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 NPC252750 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 NPC252750 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