Structure

Physi-Chem Properties

Molecular Weight:  236.07
Volume:  229.764
LogP:  1.241
LogD:  0.681
LogS:  -2.314
# Rotatable Bonds:  2
TPSA:  83.83
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.81
Synthetic Accessibility Score:  3.074
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.211
MDCK Permeability:  2.3333224817179143e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.044

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.107
Plasma Protein Binding (PPB):  59.079368591308594%
Volume Distribution (VD):  0.309
Pgp-substrate:  35.2430305480957%

ADMET: Metabolism

CYP1A2-inhibitor:  0.102
CYP1A2-substrate:  0.073
CYP2C19-inhibitor:  0.038
CYP2C19-substrate:  0.063
CYP2C9-inhibitor:  0.025
CYP2C9-substrate:  0.94
CYP2D6-inhibitor:  0.1
CYP2D6-substrate:  0.266
CYP3A4-inhibitor:  0.019
CYP3A4-substrate:  0.116

ADMET: Excretion

Clearance (CL):  13.746
Half-life (T1/2):  0.867

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.255
Drug-inuced Liver Injury (DILI):  0.959
AMES Toxicity:  0.145
Rat Oral Acute Toxicity:  0.187
Maximum Recommended Daily Dose:  0.513
Skin Sensitization:  0.667
Carcinogencity:  0.597
Eye Corrosion:  0.078
Eye Irritation:  0.421
Respiratory Toxicity:  0.817

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General Info & Identifiers & Properties  
Structure MOL file  
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  Natural Product: NPC123953

Natural Product ID:  NPC123953
Common Name*:   MONKQYHCNQSQHL-LURJTMIESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MONKQYHCNQSQHL-LURJTMIESA-N
Standard InCHI:  InChI=1S/C12H12O5/c1-6-2-9(14)12-7(4-11(15)16)3-8(13)5-10(12)17-6/h3,5-6,13H,2,4H2,1H3,(H,15,16)/p-1/t6-/m0/s1
SMILES:  C[C@H]1CC(=O)c2c(cc(cc2O1)[O-])CC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5319543
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0000144] Chromones

*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
NPO21244 Delphinium nuttallianum Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[10978210]
NPO21244 Delphinium nuttallianum Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[19012276]
NPO19996 Caulerpa peltata Species Caulerpaceae Eukaryota n.a. n.a. n.a. PMID[25593390]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20490 Erythrophleum ivorense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26917 Quercus rubra Species Fagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20144 Lespedeza tomentosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20490 Erythrophleum ivorense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13754 Tanacetum coccineum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21691 Dillenia indica Species Dilleniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20144 Lespedeza tomentosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2228 Photinia serratifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26917 Quercus rubra Species Fagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17018 Salvia greggii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20490 Erythrophleum ivorense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18867 Stephanitis takeyai Species Tingidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20353 Degenia velebitica Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20947 Tagetes filifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17568 Balanophora laxiflora Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14800 Oophaga granulifera Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12108 Aizopsis selskiana Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19232 Anchusa azurea Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19037 Senecio praecox Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13754 Tanacetum coccineum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19671 Dipsacus azureus Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11580 Onobrychis arenaria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19512 Gleichenia quadripartita Species Gleicheniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22675 Helichrysum chionosphaerum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15422 Carduus tenuiflorus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17856 Anaphalis lactea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16572 Rhododendron dahuricum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19395 Nepeta granatensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18144 Metrodorea nigra Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10359 Chaiturus marrubiastrum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21691 Dillenia indica Species Dilleniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20223 Rosa pomifera Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19996 Caulerpa peltata Species Caulerpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20422 Albizia myriophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20753 Grangea maderaspatana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14932.1 Dalbergia lanceolaria subsp. paniculata Subspecies Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27737 Penicillium shearii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20144 Lespedeza tomentosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16142 Verbascum thapsiforme Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21564 Senecio behnii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19913 Rhynchophorus ferrugineus Species Curculionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21244 Delphinium nuttallianum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24407 Bipolaris heveae Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2228 Photinia serratifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26917 Quercus rubra Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13454 Amphorogyne spicata Species Amphorogynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14248 Mandragora autumnalis Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20490 Erythrophleum ivorense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20560 Polyporus betulinus Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18287 Penicillium bilaiae Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13246 Pinalia stricta Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19818 Jacquemontia paniculata Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26393.1 Petunia integrifolia subsp. inflata Subspecies Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17018 Salvia greggii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21112 Chaetomium carinthiacum Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20625 Delphinium virgatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20844 Sphaerella rosigena n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO21376 Lupinus corymbosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10216 Leptocereus quadricostatus Species Cactaceae 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 NPC123953 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 NPC123953 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