Structure

Physi-Chem Properties

Molecular Weight:  242.08
Volume:  232.451
LogP:  -0.077
LogD:  0.3
LogS:  -1.622
# Rotatable Bonds:  5
TPSA:  96.22
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.626
Synthetic Accessibility Score:  2.715
Fsp3:  0.364
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.066
MDCK Permeability:  8.592550148023292e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.012
Human Intestinal Absorption (HIA):  0.124
20% Bioavailability (F20%):  0.016
30% Bioavailability (F30%):  0.186

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.855
Plasma Protein Binding (PPB):  48.29917526245117%
Volume Distribution (VD):  0.703
Pgp-substrate:  31.395545959472656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.077
CYP1A2-substrate:  0.508
CYP2C19-inhibitor:  0.017
CYP2C19-substrate:  0.586
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.394
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.287
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.132

ADMET: Excretion

Clearance (CL):  5.021
Half-life (T1/2):  0.927

ADMET: Toxicity

hERG Blockers:  0.083
Human Hepatotoxicity (H-HT):  0.056
Drug-inuced Liver Injury (DILI):  0.326
AMES Toxicity:  0.061
Rat Oral Acute Toxicity:  0.007
Maximum Recommended Daily Dose:  0.014
Skin Sensitization:  0.124
Carcinogencity:  0.018
Eye Corrosion:  0.003
Eye Irritation:  0.06
Respiratory Toxicity:  0.024

Download Data

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

  Natural Product: NPC68533

Natural Product ID:  NPC68533
Common Name*:   QJWLBLCJYZLCLM-SSDOTTSWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QJWLBLCJYZLCLM-SSDOTTSWSA-N
Standard InCHI:  InChI=1S/C11H14O6/c1-16-8-3-6(10(14)7(13)5-12)4-9(17-2)11(8)15/h3-4,7,12-13,15H,5H2,1-2H3/t7-/m1/s1
SMILES:  COc1cc(cc(c1O)OC)C(=O)[C@@H](CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   86311182
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003670] Aryl ketones
              • [CHEMONTID:0004296] Phenylketones
                • [CHEMONTID:0004298] Alkyl-phenylketones

*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
NPO3973 Flammulina velutipes Species Physalacriaceae Eukaryota n.a. n.a. n.a. PMID[11473426]
NPO9771 Aka coralliphagum Species Niphatidae Eukaryota n.a. San Salvador in the Bahamas (12-26 m depth) 2001-MAR; 2003-JUL PMID[17309298]
NPO13341 Bryopsis pennata Species Bryopsidaceae Eukaryota n.a. Hawaiian n.a. PMID[19916528]
NPO11402 Tithonia rotundifolia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO3973 Flammulina velutipes Species Physalacriaceae Eukaryota n.a. n.a. Database[FooDB]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17479 Aconitum tanguticum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17479 Aconitum tanguticum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27048 Pyropia tenera Species Bangiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9771 Aka coralliphagum Species Niphatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26105 Panax spinosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13341 Bryopsis pennata Species Bryopsidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13451 Pseudotsuga japonica Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18478 Vernonia scorpioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13119 Hymenoxys microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27048 Pyropia tenera Species Bangiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14637 Saussurea cordifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18218 Acanthophyllum sordidum Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4385 Aconitum zuccarini Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14222 Schefflera divaricata Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17344 Strychnos henningsii Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12356 Aphelandra chamissoniana Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11402 Tithonia rotundifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11166 Sclerodoris tanya n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO2684 Cortinarius vinosipes Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3973 Flammulina velutipes Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3026 Strophanthus hispidus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10468 Ficus beecheyana Species Ficidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11758 Parmelia pokornyi Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18809 Lyophyllum connatum Species Lyophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13834 Lecidea carpathica Species Lecideaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27114 Aconitum habaense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18724 Polyalthia stenopetala Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17479 Aconitum tanguticum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14310 Tecoma heptaphylla Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19389 Roemeria refracta Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19586 Bougainvillea glabra Species Nyctaginaceae 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 NPC68533 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 NPC68533 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