Structure

Physi-Chem Properties

Molecular Weight:  316.06
Volume:  300.063
LogP:  2.515
LogD:  2.204
LogS:  -3.841
# Rotatable Bonds:  2
TPSA:  120.36
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.572
Synthetic Accessibility Score:  2.556
Fsp3:  0.062
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  2
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.089
MDCK Permeability:  1.1116133464383893e-05
Pgp-inhibitor:  0.036
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.02
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.388

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.005
Plasma Protein Binding (PPB):  96.492431640625%
Volume Distribution (VD):  0.596
Pgp-substrate:  9.126935958862305%

ADMET: Metabolism

CYP1A2-inhibitor:  0.947
CYP1A2-substrate:  0.484
CYP2C19-inhibitor:  0.108
CYP2C19-substrate:  0.05
CYP2C9-inhibitor:  0.696
CYP2C9-substrate:  0.766
CYP2D6-inhibitor:  0.46
CYP2D6-substrate:  0.191
CYP3A4-inhibitor:  0.37
CYP3A4-substrate:  0.089

ADMET: Excretion

Clearance (CL):  6.798
Half-life (T1/2):  0.908

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.088
Drug-inuced Liver Injury (DILI):  0.986
AMES Toxicity:  0.75
Rat Oral Acute Toxicity:  0.227
Maximum Recommended Daily Dose:  0.028
Skin Sensitization:  0.8
Carcinogencity:  0.119
Eye Corrosion:  0.004
Eye Irritation:  0.906
Respiratory Toxicity:  0.088

Download Data

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

  Natural Product: NPC49901

Natural Product ID:  NPC49901
Common Name*:   AZFYHRHUTXBGJS-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  AZFYHRHUTXBGJS-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H12O7/c1-22-15-10(19)6-9(18)11-12(20)13(21)14(23-16(11)15)7-2-4-8(17)5-3-7/h2-6,17-19,21H,1H3
SMILES:  COc1c(cc(c2c(=O)c(c(c3ccc(cc3)O)oc12)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5281698
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001615] Flavones
          • [CHEMONTID:0001136] Flavonols

*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
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[18177011]
NPO25429 Sorbus aria Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[18635332]
NPO13029 Sorbus aucuparia Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[18635332]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[19271742]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO9756 Daphne genkwa Species Thymelaeaceae Eukaryota n.a. flower n.a. PMID[21916433]
NPO9756 Daphne genkwa Species Thymelaeaceae Eukaryota flower buds n.a. n.a. PMID[23558238]
NPO9756 Daphne genkwa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[27228307]
NPO9756 Daphne genkwa Species Thymelaeaceae Eukaryota Roots n.a. n.a. PMID[31150241]
NPO9756 Daphne genkwa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[31860304]
NPO9756 Daphne genkwa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[32223193]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO13029 Sorbus aucuparia Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9756 Daphne genkwa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19039 Pholidota articulata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13029 Sorbus aucuparia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13029 Sorbus aucuparia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9756 Daphne genkwa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19039 Pholidota articulata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13029 Sorbus aucuparia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9756 Daphne genkwa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9756 Daphne genkwa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28162 Gouania leptostachya Species Gobiesocidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25429 Sorbus aria Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9756 Daphne genkwa Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18365 Osteospermum rigidum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13029 Sorbus aucuparia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18225 Agrotis fucosa Species 0ctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19039 Pholidota articulata Species Orchidaceae 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 NPC49901 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 NPC49901 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