Structure

Physi-Chem Properties

Molecular Weight:  344.16
Volume:  356.939
LogP:  3.568
LogD:  3.319
LogS:  -3.774
# Rotatable Bonds:  2
TPSA:  79.9
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.633
Synthetic Accessibility Score:  6.528
Fsp3:  0.45
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.888
MDCK Permeability:  6.0897211369592696e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.938
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.387
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.173
Plasma Protein Binding (PPB):  80.85912322998047%
Volume Distribution (VD):  1.815
Pgp-substrate:  14.024181365966797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.032
CYP1A2-substrate:  0.598
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.145
CYP2C9-inhibitor:  0.066
CYP2C9-substrate:  0.123
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.064
CYP3A4-inhibitor:  0.149
CYP3A4-substrate:  0.361

ADMET: Excretion

Clearance (CL):  13.597
Half-life (T1/2):  0.15

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.634
Drug-inuced Liver Injury (DILI):  0.127
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.923
Maximum Recommended Daily Dose:  0.968
Skin Sensitization:  0.419
Carcinogencity:  0.927
Eye Corrosion:  0.039
Eye Irritation:  0.058
Respiratory Toxicity:  0.967

Download Data

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

  Natural Product: NPC11153

Natural Product ID:  NPC11153
Common Name*:   QFEYDWNEIMUBOK-YTRSDULBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QFEYDWNEIMUBOK-YTRSDULBSA-N
Standard InCHI:  InChI=1S/C20H24O5/c1-10(2)13-7-6-12-8-14(24-18(12)22)16(11(3)4)15-9-20(5,17(13)21)19(23)25-15/h8-9,13-14,16-17,21H,1,3,6-7H2,2,4-5H3/t13-,14+,16+,17-,20-/m0/s1
SMILES:  C=C(C)[C@@H]1CCC2=C[C@H]([C@@H](C(=C)C)C3=C[C@@](C)([C@H]1O)C(=O)O3)OC2=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10980852
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones

*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
NPO15684 Cochliobolus heterostrophus Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[10395513]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[15182859]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. root n.a. PMID[16310231]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. root n.a. PMID[16651783]
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[21090694]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. stem n.a. PMID[21428375]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[23599008]
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[24175613]
NPO20005 Penstemon barbatus Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[26351040]
NPO1448 Diospyros lycioides Species Ebenaceae Eukaryota n.a. n.a. n.a. PMID[9644074]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8735 Berberis poiretii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18878.1 Amaranthus blitum subsp. oleraceus Subspecies Amaranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8735 Berberis poiretii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8735 Berberis poiretii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21817 Riccardia chamedryfolia Species Aneuraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24985 Lippia asperifolia Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24210 Senecio heterotrichus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18878.1 Amaranthus blitum subsp. oleraceus Subspecies Amaranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24928 Cratoxylum cochinchinense Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12235 Trachelospermum jasminoides Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24741 Psathyrella scobinacea Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15326 Paranemertes peregrina Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15684 Cochliobolus heterostrophus Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18873.7 Salmonella enterica subsp. enterica serovar typhi Subspecies Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO20005 Penstemon barbatus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24474 Rhododendron lepidotum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20129 Salicornia europaea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23799 Gentiana triflora Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25442 Isocoma tenuisecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25527 Tephrosia multijuga Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19851 Miconia stenostachya Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17597 Cassia fistulosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8735 Berberis poiretii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25042 Fusarium tricinctum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1448 Diospyros lycioides Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21476 Pterogorgia kallos Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24787 Astragalus babatagi Species 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 NPC11153 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 NPC11153 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