Structure

Physi-Chem Properties

Molecular Weight:  313.1
Volume:  310.775
LogP:  1.522
LogD:  1.214
LogS:  -3.382
# Rotatable Bonds:  3
TPSA:  88.62
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.849
Synthetic Accessibility Score:  3.65
Fsp3:  0.176
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:  -4.885
MDCK Permeability:  1.1731152881111484e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.066
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.023

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.627
Plasma Protein Binding (PPB):  88.24298858642578%
Volume Distribution (VD):  1.059
Pgp-substrate:  13.085274696350098%

ADMET: Metabolism

CYP1A2-inhibitor:  0.7
CYP1A2-substrate:  0.786
CYP2C19-inhibitor:  0.681
CYP2C19-substrate:  0.4
CYP2C9-inhibitor:  0.77
CYP2C9-substrate:  0.973
CYP2D6-inhibitor:  0.109
CYP2D6-substrate:  0.859
CYP3A4-inhibitor:  0.702
CYP3A4-substrate:  0.233

ADMET: Excretion

Clearance (CL):  3.206
Half-life (T1/2):  0.776

ADMET: Toxicity

hERG Blockers:  0.163
Human Hepatotoxicity (H-HT):  0.561
Drug-inuced Liver Injury (DILI):  0.355
AMES Toxicity:  0.039
Rat Oral Acute Toxicity:  0.844
Maximum Recommended Daily Dose:  0.982
Skin Sensitization:  0.569
Carcinogencity:  0.101
Eye Corrosion:  0.003
Eye Irritation:  0.094
Respiratory Toxicity:  0.926

Download Data

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

  Natural Product: NPC42051

Natural Product ID:  NPC42051
Common Name*:   NVUHVZUPJHEJGT-CWDCEQMOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NVUHVZUPJHEJGT-CWDCEQMOSA-N
Standard InCHI:  InChI=1S/C17H15NO5/c1-3-4-9-5-13(20)12(8-18-9)16-15-11(17(21)23-16)6-10(19)7-14(15)22-2/h3-8,16,19H,1-2H3,(H,18,20)/b4-3+/t16-/m0/s1
SMILES:  C/C=C/c1cc(=O)c(c[nH]1)[C@H]1c2c(cc(cc2OC)O)C(=O)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   24761001
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000301] Benzofurans
        • [CHEMONTID:0001578] Benzofuranones

*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
NPO18252 Cajanus cajan Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[136119]
NPO16746 Lendenfeldia frondosa Species Thorectidae Eukaryota n.a. n.a. n.a. PMID[1402955]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota n.a. leaf n.a. PMID[24680612]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO18659 Prunus japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19073 Uncaria lancifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16040 Pristimera indica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO3022 Toxicopueraria peduncularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19073 Uncaria lancifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16040 Pristimera indica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18659 Prunus japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11777 Pluchea sericea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18659 Prunus japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18659 Prunus japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19753 Liabum bourgeaui Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14711.1 Arabidopsis lyrata subsp. lyrata Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16040 Pristimera indica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19073 Uncaria lancifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23370 Sticta mougeotiana Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29099 Sinocrassula indica Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19692 Quercus variabilis Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11042 Lecanora sordida Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11777 Pluchea sericea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16746 Lendenfeldia frondosa Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28174 Poterium sanguisorba Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18659 Prunus japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18008 Viburnum rhytidophyllum Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13673 Ipomoea muelleri Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6425 Betula davurica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3022 Toxicopueraria peduncularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18497 Euphorbia aellenii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19229 Aniba parviflora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14953 Thapsia transtagana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15430 Abutilon grandiflorum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17440 Thryptomene kochii Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18830 Valeriana cardamines Species Caprifoliaceae 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 NPC42051 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 NPC42051 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