Structure

Physi-Chem Properties

Molecular Weight:  632.39
Volume:  651.076
LogP:  3.011
LogD:  3.025
LogS:  -4.043
# Rotatable Bonds:  5
TPSA:  156.91
# H-Bond Aceptor:  9
# H-Bond Donor:  6
# Rings:  6
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.202
Synthetic Accessibility Score:  5.582
Fsp3:  0.861
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.517
MDCK Permeability:  1.0954913705063518e-05
Pgp-inhibitor:  0.065
Pgp-substrate:  0.024
Human Intestinal Absorption (HIA):  0.155
20% Bioavailability (F20%):  0.108
30% Bioavailability (F30%):  0.162

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.057
Plasma Protein Binding (PPB):  85.38270568847656%
Volume Distribution (VD):  0.743
Pgp-substrate:  8.787306785583496%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.631
CYP2C19-inhibitor:  0.002
CYP2C19-substrate:  0.679
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.02
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.066
CYP3A4-inhibitor:  0.635
CYP3A4-substrate:  0.129

ADMET: Excretion

Clearance (CL):  2.096
Half-life (T1/2):  0.209

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.212
Drug-inuced Liver Injury (DILI):  0.033
AMES Toxicity:  0.03
Rat Oral Acute Toxicity:  0.91
Maximum Recommended Daily Dose:  0.973
Skin Sensitization:  0.119
Carcinogencity:  0.086
Eye Corrosion:  0.004
Eye Irritation:  0.013
Respiratory Toxicity:  0.986

Download Data

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

  Natural Product: NPC107638

Natural Product ID:  NPC107638
Common Name*:   CNXVDVMAYXLWPD-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CNXVDVMAYXLWPD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C19H11NO4/c1-2-12-11-3-4-15-19(24-9-21-15)14(11)7-20-18(12)13-6-17-16(5-10(1)13)22-8-23-17/h1-7H,8-9H2
SMILES:  c1cc2c3ccc4c(c3cnc2c2cc3c(cc12)OCO3)OCO4
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   97679
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
NPO20958 Smenospongia aurea Species Thorectidae Eukaryota n.a. Jamaican n.a. PMID[11975483]
NPO20254 Ipomoea leptophylla Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[14640518]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[15019787]
NPO22556 Dendrolobium lanceolatum Species Fabaceae Eukaryota n.a. root n.a. PMID[15217275]
NPO927 Swertia mussotii Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[19645233]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[22029392]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[23517479]
NPO927 Swertia mussotii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota Latex Exudate n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. Database[FooDB]
NPO927 Swertia mussotii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7672 Senna tora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8543 Meconopsis horridula Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO927 Swertia mussotii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19361 Herba meconpsis integrifoliae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7672 Senna tora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22495 Cladonia alpestris Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7312 Aplidium multiplicatum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18257 Oberna wallichiana n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO17360 Argemone albiflora Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO927 Swertia mussotii Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8543 Meconopsis horridula Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2466 Aloe microstigma Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14326 Pseudocercospora fijiensis Species Mycosphaerellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22817 Actinidia valvata Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22556 Dendrolobium lanceolatum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21026 Pericopsis mooniana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10176 Chrozophora prostrata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7672 Senna tora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20254 Ipomoea leptophylla Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18680 Larix decidua Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20958 Smenospongia aurea Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21848 Rosa hybr Species Rosaceae 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
NPT81 Cell Line A549 Homo sapiens IC50 > 30000.0 nM PMID[553465]
NPT2341 Cell Line NCI-H1975 Homo sapiens IC50 > 30000.0 nM PMID[553465]

☑ 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 NPC107638 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 NPC107638 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