Structure

Physi-Chem Properties

Molecular Weight:  348.27
Volume:  390.417
LogP:  5.122
LogD:  4.33
LogS:  -4.434
# Rotatable Bonds:  3
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.561
Synthetic Accessibility Score:  5.016
Fsp3:  0.773
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.595
MDCK Permeability:  3.316317452117801e-05
Pgp-inhibitor:  0.955
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.78
20% Bioavailability (F20%):  0.462
30% Bioavailability (F30%):  0.883

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.555
Plasma Protein Binding (PPB):  91.0503921508789%
Volume Distribution (VD):  1.012
Pgp-substrate:  3.6438851356506348%

ADMET: Metabolism

CYP1A2-inhibitor:  0.044
CYP1A2-substrate:  0.085
CYP2C19-inhibitor:  0.103
CYP2C19-substrate:  0.66
CYP2C9-inhibitor:  0.188
CYP2C9-substrate:  0.383
CYP2D6-inhibitor:  0.345
CYP2D6-substrate:  0.18
CYP3A4-inhibitor:  0.745
CYP3A4-substrate:  0.364

ADMET: Excretion

Clearance (CL):  3.16
Half-life (T1/2):  0.339

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.455
Drug-inuced Liver Injury (DILI):  0.561
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.044
Maximum Recommended Daily Dose:  0.95
Skin Sensitization:  0.948
Carcinogencity:  0.073
Eye Corrosion:  0.118
Eye Irritation:  0.468
Respiratory Toxicity:  0.195

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

  Natural Product: NPC55913

Natural Product ID:  NPC55913
Common Name*:   QPIUBKNTZMBLLI-ZEWQPTNTSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QPIUBKNTZMBLLI-ZEWQPTNTSA-N
Standard InCHI:  InChI=1S/C22H36O3/c1-15-8-7-9-16(2)14-19(25-17(3)23)20-18(21(4,5)24)11-13-22(20,6)12-10-15/h9-10,12,15,18-20,24H,7-8,11,13-14H2,1-6H3/b12-10+,16-9+/t15-,18+,19-,20+,22-/m0/s1
SMILES:  C[C@H]1CC/C=C(C)/C[C@@H]([C@H]2[C@@H](CC[C@]2(C)/C=C/1)C(C)(C)O)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0001760] Dolabellane and neodolabellane diterpenoids

*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
NPO21169 Salvia blepharochlaena Species Lamiaceae Eukaryota roots n.a. n.a. PMID[11325249]
NPO29285 Dendrobium densiflorum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18865 Tetracentron sinense Species Trochodendraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21306 Alpinia pinnanensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29285 Dendrobium densiflorum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21306 Alpinia pinnanensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29146 Polygonatum kingianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18865 Tetracentron sinense Species Trochodendraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29146 Polygonatum kingianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29146 Polygonatum kingianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29285 Dendrobium densiflorum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20221 Maytenus truncata Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20420 Helenium brevifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21494 Eryngium maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29313 Halomonas meridiana Species Halomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29146 Polygonatum kingianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27967 Betula glandulosa Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16565 Lindera oldhami Species Tineidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19911 Arachniodes festina Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20838 Cleome pentaphylla Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17330 Pseudopotamilla occelata Species Sabellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17838 Aster flaccidus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20488 Abies homolepis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21306 Alpinia pinnanensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21169 Salvia blepharochlaena Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29308 Mycobacterium marinum Species Mycobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO20558 Pseudevernia ericetorum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18865 Tetracentron sinense Species Trochodendraceae 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 NPC55913 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 NPC55913 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