Structure

Physi-Chem Properties

Molecular Weight:  298.08
Volume:  299.778
LogP:  4.072
LogD:  2.654
LogS:  -3.407
# Rotatable Bonds:  1
TPSA:  101.15
# H-Bond Aceptor:  5
# H-Bond Donor:  5
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.349
Synthetic Accessibility Score:  2.915
Fsp3:  0.059
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.329
MDCK Permeability:  6.973985819058726e-06
Pgp-inhibitor:  0.007
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.054
20% Bioavailability (F20%):  0.804
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.006
Plasma Protein Binding (PPB):  97.45679473876953%
Volume Distribution (VD):  0.554
Pgp-substrate:  5.110006809234619%

ADMET: Metabolism

CYP1A2-inhibitor:  0.97
CYP1A2-substrate:  0.366
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.053
CYP2C9-inhibitor:  0.55
CYP2C9-substrate:  0.707
CYP2D6-inhibitor:  0.123
CYP2D6-substrate:  0.365
CYP3A4-inhibitor:  0.109
CYP3A4-substrate:  0.047

ADMET: Excretion

Clearance (CL):  10.48
Half-life (T1/2):  0.863

ADMET: Toxicity

hERG Blockers:  0.023
Human Hepatotoxicity (H-HT):  0.321
Drug-inuced Liver Injury (DILI):  0.634
AMES Toxicity:  0.572
Rat Oral Acute Toxicity:  0.105
Maximum Recommended Daily Dose:  0.932
Skin Sensitization:  0.961
Carcinogencity:  0.362
Eye Corrosion:  0.01
Eye Irritation:  0.928
Respiratory Toxicity:  0.48

Download Data

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

  Natural Product: NPC284372

Natural Product ID:  NPC284372
Common Name*:   XJZIVQGVSOVEOC-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XJZIVQGVSOVEOC-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C17H14O5/c1-2-3-8-4-10-14(12(19)5-8)17(22)15-11(16(10)21)6-9(18)7-13(15)20/h4-7,18-20H,2-3H2,1H3
SMILES:  CCCc1cc2c(c(c1)O)C(=O)c1c(cc(cc1O)O)C2=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   23265983
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000018] Anthracenes
        • [CHEMONTID:0000151] Anthraquinones
          • [CHEMONTID:0001598] Hydroxyanthraquinones

*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
NPO13814 Tupidanthus calyptratus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[11421737]
NPO28679 Prunus mume Species Rosaceae Eukaryota flowers n.a. n.a. PMID[12193020]
NPO28888 Magnaporthe grisea Species Magnaporthaceae Eukaryota n.a. n.a. n.a. PMID[16869509]
NPO28679 Prunus mume Species Rosaceae Eukaryota fruits n.a. n.a. PMID[24485782]
NPO28836 Gypsophila pacifica Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26271 Physochlaina infundibularis Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28874 Rhododendron fauriei Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13914 Fraxinus ornus Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13914 Fraxinus ornus Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28836 Gypsophila pacifica Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26271 Physochlaina infundibularis Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28874 Rhododendron fauriei Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18207 Radermachera sinica Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13914 Fraxinus ornus Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28836 Gypsophila pacifica Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11691 Limnothrix rosea Species Pseudanabaenaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14510 Streptomyces acidiscabies Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13088 Vicia pseudo-orobus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2159 Helipterum splendidum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25557 Alternaria porri Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13914 Fraxinus ornus Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1488 Aphis spiraecola Species Aphididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14838 Myriocephalus stuartii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18207 Radermachera sinica Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9689 Pertusaria flavicans Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14006 Halostachys caspica Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26271 Physochlaina infundibularis Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28874 Rhododendron fauriei Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9076 Tiliacora dinklagei Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13814 Tupidanthus calyptratus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22644 Helichrysum argenteum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2586 Alnus rubra Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8371 Fagara rhoifolia n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO4309 Carapa procera Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5467 Helenium campestre Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28888 Magnaporthe grisea Species Magnaporthaceae 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 NPC284372 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 NPC284372 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