Structure

Physi-Chem Properties

Molecular Weight:  248.14
Volume:  260.788
LogP:  1.967
LogD:  2.286
LogS:  -3.205
# Rotatable Bonds:  0
TPSA:  43.37
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.488
Synthetic Accessibility Score:  4.315
Fsp3:  0.733
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.67
MDCK Permeability:  2.707286512304563e-05
Pgp-inhibitor:  0.046
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.431
30% Bioavailability (F30%):  0.02

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.159
Plasma Protein Binding (PPB):  86.43347930908203%
Volume Distribution (VD):  0.788
Pgp-substrate:  12.968347549438477%

ADMET: Metabolism

CYP1A2-inhibitor:  0.326
CYP1A2-substrate:  0.617
CYP2C19-inhibitor:  0.358
CYP2C19-substrate:  0.778
CYP2C9-inhibitor:  0.286
CYP2C9-substrate:  0.558
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.463
CYP3A4-inhibitor:  0.472
CYP3A4-substrate:  0.332

ADMET: Excretion

Clearance (CL):  8.107
Half-life (T1/2):  0.83

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.353
Drug-inuced Liver Injury (DILI):  0.649
AMES Toxicity:  0.101
Rat Oral Acute Toxicity:  0.37
Maximum Recommended Daily Dose:  0.611
Skin Sensitization:  0.811
Carcinogencity:  0.852
Eye Corrosion:  0.703
Eye Irritation:  0.92
Respiratory Toxicity:  0.884

Download Data

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

  Natural Product: NPC7257

Natural Product ID:  NPC7257
Common Name*:   DCKYPAZZUYXYTC-ZGWNKZGNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DCKYPAZZUYXYTC-ZGWNKZGNSA-N
Standard InCHI:  InChI=1S/C15H20O3/c1-8-6-12-10(9(2)14(17)18-12)7-15(3)11(8)4-5-13(15)16/h8,10-12H,2,4-7H2,1,3H3/t8-,10+,11-,12+,15+/m0/s1
SMILES:  C[C@H]1C[C@@H]2[C@H](C[C@]3(C)[C@H]1CCC3=O)C(=C)C(=O)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   24893981
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001543] Sesquiterpene lactones
            • [CHEMONTID:0002046] Ambrosanolides and secoambrosanolides

*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
NPO10541 Dioscorea spongiosa Species Dioscoreaceae Eukaryota rhizomes n.a. n.a. PMID[12762799]
NPO19126 Lycopodium sieboldii Species Lycopodiaceae Eukaryota n.a. n.a. n.a. PMID[14535761]
NPO17553 Pleione bulbocodioides Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[23627123]
NPO20442 Croton stellatopilosus Species Euphorbiaceae Eukaryota n.a. leaf n.a. PMID[24286075]
NPO10023 Francoeuria undulata Species Asteraceae Eukaryota Aerial Parts n.a. n.a. PMID[28032767]
NPO16284 Scutellaria galericulata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10541 Dioscorea spongiosa Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10541 Dioscorea spongiosa Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21204 Achillea holosericea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16284 Scutellaria galericulata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17553 Pleione bulbocodioides Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17553 Pleione bulbocodioides Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16284 Scutellaria galericulata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20628 Magnolia kachirachirai Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18555 Vernonia chinensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19126 Lycopodium sieboldii Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20185 Lachnanthes tinctoria Species Haemodoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10541 Dioscorea spongiosa Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17553 Pleione bulbocodioides Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10023 Francoeuria undulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4239 Betula neoalaskana Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19875 Ceratocystis ips Species Ceratocystidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20442 Croton stellatopilosus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8004 Hexaplex trunculus Species Muricidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21204 Achillea holosericea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19665 Salvia aerea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20071 Dracaena cinnabari Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21018 Macrozamia riedlei Species Zamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21330 Ilex integra Species Aquifoliaceae 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 NPC7257 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 NPC7257 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