Structure

Physi-Chem Properties

Molecular Weight:  265.07
Volume:  267.342
LogP:  3.025
LogD:  3.226
LogS:  -5.904
# Rotatable Bonds:  1
TPSA:  50.94
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.538
Synthetic Accessibility Score:  2.329
Fsp3:  0.062
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.795
MDCK Permeability:  2.2136793631943874e-05
Pgp-inhibitor:  0.007
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.031
20% Bioavailability (F20%):  0.069
30% Bioavailability (F30%):  0.504

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.329
Plasma Protein Binding (PPB):  93.39910888671875%
Volume Distribution (VD):  0.475
Pgp-substrate:  3.9050116539001465%

ADMET: Metabolism

CYP1A2-inhibitor:  0.961
CYP1A2-substrate:  0.876
CYP2C19-inhibitor:  0.786
CYP2C19-substrate:  0.251
CYP2C9-inhibitor:  0.547
CYP2C9-substrate:  0.885
CYP2D6-inhibitor:  0.525
CYP2D6-substrate:  0.867
CYP3A4-inhibitor:  0.537
CYP3A4-substrate:  0.188

ADMET: Excretion

Clearance (CL):  10.596
Half-life (T1/2):  0.345

ADMET: Toxicity

hERG Blockers:  0.046
Human Hepatotoxicity (H-HT):  0.815
Drug-inuced Liver Injury (DILI):  0.937
AMES Toxicity:  0.945
Rat Oral Acute Toxicity:  0.122
Maximum Recommended Daily Dose:  0.934
Skin Sensitization:  0.547
Carcinogencity:  0.961
Eye Corrosion:  0.003
Eye Irritation:  0.813
Respiratory Toxicity:  0.411

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

  Natural Product: NPC28624

Natural Product ID:  NPC28624
Common Name*:   LAKWSSVAGFQTAY-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LAKWSSVAGFQTAY-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H11NO3/c1-20-14-8-11-10-4-2-3-9-5-6-17(15(9)10)16(19)12(11)7-13(14)18/h2-8,18H,1H3
SMILES:  COc1cc2c3cccc4ccn(c34)c(=O)c2cc1O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   181937
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001253] Quinolines and derivatives
        • [CHEMONTID:0001908] Benzoquinolines
          • [CHEMONTID:0000100] Phenanthridines and derivatives

*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
NPO22157 Datura wrightii Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[23252848]
NPO22054 Cinchona officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3630 Crotalaria crispata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9927.1 Crinum asiaticum var. japonicum Varieties Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1383.1 Murraya paniculata var. omphalocarpa Varieties Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22054 Cinchona officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9927.1 Crinum asiaticum var. japonicum Varieties Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3630 Crotalaria crispata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20170 Anthoceros punctatus Species Anthocerotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3630 Crotalaria crispata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23120 Clausena suffruticosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22157 Datura wrightii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22054 Cinchona officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10342 Crinum americanum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1412 Artemisia juncea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22009 Lupinus holosericeus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19776 Hesperocyparis arizonica Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9485 Haplopappus deserticola Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1383.1 Murraya paniculata var. omphalocarpa Varieties Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9144 Atriplex parvifolia Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11000 Eupatorium laevigatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13659 Helichrysum asperum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23036 Angelica hirsutiflora Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11473 Viburnum lantana Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18476 Lophopetalum toxicum Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1828 Searsia leptodictya Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21442 Elaeocarpus sphaericus Species Elaeocarpaceae 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
NPT179 Cell Line A2780 Homo sapiens IC50 > 75000.0 nM PMID[520387]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 38000.0 nM PMID[520387]

☑ 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 NPC28624 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 NPC28624 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