Structure

Physi-Chem Properties

Molecular Weight:  204.19
Volume:  245.61
LogP:  5.661
LogD:  4.757
LogS:  -4.963
# Rotatable Bonds:  1
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.548
Synthetic Accessibility Score:  4.298
Fsp3:  0.733
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:  -4.413
MDCK Permeability:  1.74141168827191e-05
Pgp-inhibitor:  0.179
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.999
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.15
Plasma Protein Binding (PPB):  96.28548431396484%
Volume Distribution (VD):  4.77
Pgp-substrate:  3.2172367572784424%

ADMET: Metabolism

CYP1A2-inhibitor:  0.853
CYP1A2-substrate:  0.74
CYP2C19-inhibitor:  0.604
CYP2C19-substrate:  0.914
CYP2C9-inhibitor:  0.653
CYP2C9-substrate:  0.389
CYP2D6-inhibitor:  0.146
CYP2D6-substrate:  0.551
CYP3A4-inhibitor:  0.804
CYP3A4-substrate:  0.381

ADMET: Excretion

Clearance (CL):  11.775
Half-life (T1/2):  0.125

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.17
Drug-inuced Liver Injury (DILI):  0.814
AMES Toxicity:  0.014
Rat Oral Acute Toxicity:  0.106
Maximum Recommended Daily Dose:  0.078
Skin Sensitization:  0.081
Carcinogencity:  0.725
Eye Corrosion:  0.179
Eye Irritation:  0.584
Respiratory Toxicity:  0.469

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

  Natural Product: NPC106452

Natural Product ID:  NPC106452
Common Name*:   AKKNWGRLXKHQDH-QWHCGFSZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  AKKNWGRLXKHQDH-QWHCGFSZSA-N
Standard InCHI:  InChI=1S/C13H20O2/c1-11(2)6-4-5-10-9-14-12(3)7-8-13(10,11)15-12/h5H,4,6-9H2,1-3H3/t12-,13+/m0/s1
SMILES:  CC1(C)CCC=C2CO[C@]3(C)CC[C@]12O3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001729] Oxepanes

*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
NPO22761 Gentiana cruciata Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)88887-1]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. DOI[10.1071/CH03175]
NPO14117 Diplodia sapinea Species Botryosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[10075753]
NPO24512 Xestospongia testudinaria Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[10543913]
NPO25046 Aplidium meridianum Species Polyclinidae Eukaryota n.a. South Georgia Islands, South Atlantic n.a. PMID[15026054]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO25391 Vitex glabrata Species Lamiaceae Eukaryota leaves Chantaburi Province, Thailand 2007-Nov PMID[19943620]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota twigs n.a. n.a. PMID[20058933]
NPO28887 Eupomatia laurina Species Eupomatiaceae Eukaryota n.a. n.a. n.a. PMID[21504145]
NPO24745 Salvia cavaleriei Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24256484]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota flowers Pakook, Muang District, Chiang Rai Province, Thailand 2013-Feb PMID[25651042]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota young fruits Khokkhon, Tha Bo District, Nong Khai Province, Thailand 2011-Aug PMID[25651042]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[27128898]
NPO22780 Sphaeranthus africanus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[30074787]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota Leaves n.a. n.a. PMID[31860303]
NPO25046 Aplidium meridianum Species Polyclinidae Eukaryota n.a. n.a. n.a. PMID[9748381]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13767 Woodfordia fruticosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24077 Astragalus pterocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO13767 Woodfordia fruticosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24077 Astragalus pterocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23568 Guatteria pogonopus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18842 Gnaphalium gaudichaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25625 Hymenophyllum recurvum Species Hymenophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25364 Didemnum candidum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22761 Gentiana cruciata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22293 Bryobium hyacinthoides Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24512 Xestospongia testudinaria Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25391 Vitex glabrata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24077 Astragalus pterocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25046 Aplidium meridianum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13767 Woodfordia fruticosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5027 Peniophora polygonia Species Peniophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22780 Sphaeranthus africanus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25091 Samadera bidwillii Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14117 Diplodia sapinea Species Botryosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25700 Psiadia punctulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28887 Eupomatia laurina Species Eupomatiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24745 Salvia cavaleriei Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25472 Garcinia cowa Species Clusiaceae 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 NPC106452 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 NPC106452 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