Structure

Physi-Chem Properties

Molecular Weight:  510.13
Volume:  509.509
LogP:  6.053
LogD:  2.731
LogS:  -4.747
# Rotatable Bonds:  3
TPSA:  161.84
# H-Bond Aceptor:  8
# H-Bond Donor:  8
# Rings:  6
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.151
Synthetic Accessibility Score:  2.947
Fsp3:  0.067
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.097
MDCK Permeability:  5.900182259210851e-06
Pgp-inhibitor:  0.026
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  1.0
20% Bioavailability (F20%):  0.842
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  94.26590728759766%
Volume Distribution (VD):  0.465
Pgp-substrate:  10.992453575134277%

ADMET: Metabolism

CYP1A2-inhibitor:  0.886
CYP1A2-substrate:  0.101
CYP2C19-inhibitor:  0.062
CYP2C19-substrate:  0.044
CYP2C9-inhibitor:  0.577
CYP2C9-substrate:  0.459
CYP2D6-inhibitor:  0.029
CYP2D6-substrate:  0.232
CYP3A4-inhibitor:  0.04
CYP3A4-substrate:  0.03

ADMET: Excretion

Clearance (CL):  3.938
Half-life (T1/2):  0.426

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.027
Drug-inuced Liver Injury (DILI):  0.98
AMES Toxicity:  0.493
Rat Oral Acute Toxicity:  0.016
Maximum Recommended Daily Dose:  0.606
Skin Sensitization:  0.958
Carcinogencity:  0.065
Eye Corrosion:  0.003
Eye Irritation:  0.917
Respiratory Toxicity:  0.049

Download Data

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

  Natural Product: NPC63293

Natural Product ID:  NPC63293
Common Name*:   UKTUEGXCIOJVKY-PSWAGMNNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  UKTUEGXCIOJVKY-PSWAGMNNSA-N
Standard InCHI:  InChI=1S/C30H22O8/c31-11-13-7-17-23(15-3-1-5-19(33)25(15)29(37)27(17)21(35)9-13)24-16-4-2-6-20(34)26(16)30(38)28-18(24)8-14(12-32)10-22(28)36/h1-10,23-24,31-36H,11-12H2/t23-,24+
SMILES:  c1cc2[C@@H](c3cc(cc(c3C(=O)c2c(c1)O)O)CO)[C@@H]1c2cccc(c2C(=O)c2c1cc(cc2O)CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000018] Anthracenes

*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
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. n.a. n.a. PMID[11087602]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. stem n.a. PMID[12932124]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. n.a. n.a. PMID[12932124]
NPO27164 Aspergillus alliaceus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[29517220]
NPO27164 Aspergillus alliaceus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[3417561]
NPO30631 Rhamnus frangula Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3980 Frangula purshiana Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19050 Garcinia polyantha Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27140 Amanita phalloides Species Amanitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30631 Rhamnus frangula Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24629 Achromobacter denitrificans Species Alcaligenaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO3980 Frangula purshiana Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27790 Delia arenicola Species Anthomyiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19050 Garcinia polyantha Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4132 Cranfillia fluviatilis Species Blechnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27454 Turbo cornutus Species Turbinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27164 Aspergillus alliaceus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26972 Baccharis potosina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27873 Ravenia spectabilis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17822 Fridericia triplinervia Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27564 Stevia berlandieri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10239 Magnolia figo Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27140 Amanita phalloides Species Amanitaceae 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 NPC63293 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 NPC63293 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