Structure

Physi-Chem Properties

Molecular Weight:  330.11
Volume:  328.501
LogP:  3.929
LogD:  3.138
LogS:  -3.672
# Rotatable Bonds:  4
TPSA:  96.22
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.749
Synthetic Accessibility Score:  3.051
Fsp3:  0.278
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:  -4.883
MDCK Permeability:  1.6920403140829876e-05
Pgp-inhibitor:  0.007
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.18

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.045
Plasma Protein Binding (PPB):  97.71968841552734%
Volume Distribution (VD):  0.582
Pgp-substrate:  1.957951545715332%

ADMET: Metabolism

CYP1A2-inhibitor:  0.936
CYP1A2-substrate:  0.708
CYP2C19-inhibitor:  0.893
CYP2C19-substrate:  0.065
CYP2C9-inhibitor:  0.849
CYP2C9-substrate:  0.954
CYP2D6-inhibitor:  0.783
CYP2D6-substrate:  0.696
CYP3A4-inhibitor:  0.506
CYP3A4-substrate:  0.209

ADMET: Excretion

Clearance (CL):  14.253
Half-life (T1/2):  0.603

ADMET: Toxicity

hERG Blockers:  0.106
Human Hepatotoxicity (H-HT):  0.061
Drug-inuced Liver Injury (DILI):  0.487
AMES Toxicity:  0.218
Rat Oral Acute Toxicity:  0.246
Maximum Recommended Daily Dose:  0.22
Skin Sensitization:  0.93
Carcinogencity:  0.305
Eye Corrosion:  0.003
Eye Irritation:  0.904
Respiratory Toxicity:  0.106

Download Data

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

  Natural Product: NPC117091

Natural Product ID:  NPC117091
Common Name*:   KDJZPCLLOPNECJ-HNNXBMFYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KDJZPCLLOPNECJ-HNNXBMFYSA-N
Standard InCHI:  InChI=1S/C18H18O6/c1-2-23-18(22)16-14(21)9-13(20)12-7-8-15(24-17(12)16)10-3-5-11(19)6-4-10/h3-6,9,15,19-21H,2,7-8H2,1H3/t15-/m0/s1
SMILES:  CCOC(=O)c1c(cc(c2CC[C@@H](c3ccc(cc3)O)Oc12)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002991] Hydroxyflavonoids
          • [CHEMONTID:0002993] 7-hydroxyflavonoids

*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
NPO19803 Oxytropis ochrocephala Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22494026]
NPO14508 Aconitum heterophyllum Species Ranunculaceae Eukaryota n.a. root n.a. PMID[24156713]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[32997496]
NPO19303 Auricularia auricula-judae Species Auriculariaceae Eukaryota n.a. n.a. Database[FooDB]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14508 Aconitum heterophyllum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18816 Lindera glauca Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19303 Auricularia auricula-judae Species Auriculariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14508 Aconitum heterophyllum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18816 Lindera glauca Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18393 Eugenia sandwicensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16416 Serratula strangulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19303 Auricularia auricula-judae Species Auriculariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19406 Chrysanthemum leptophyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13505 Grateloupia livida Species Halymeniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4035 Daphne odora Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19479 Trametes feei Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19303 Auricularia auricula-judae Species Auriculariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14015 Salacia cordata Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15287 Vernonia megapotamica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10705 Marshallia graminifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10882 Acer caudatifolium Species Aceraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12376 Baccharis macraei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12444 Astragalus sinicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19803 Oxytropis ochrocephala Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17558 Cynoglossum formosanum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7037 Rumohra adiantiformis Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18816 Lindera glauca Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18393 Eugenia sandwicensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17135 Mikania goyazensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16416 Serratula strangulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14508 Aconitum heterophyllum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18247 Globicephala melas Species Delphinidae 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 NPC117091 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 NPC117091 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