Structure

Physi-Chem Properties

Molecular Weight:  272.1
Volume:  284.885
LogP:  3.051
LogD:  3.161
LogS:  -3.436
# Rotatable Bonds:  5
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.821
Synthetic Accessibility Score:  1.975
Fsp3:  0.188
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.777
MDCK Permeability:  1.6963113012025133e-05
Pgp-inhibitor:  0.018
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.966
30% Bioavailability (F30%):  0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.137
Plasma Protein Binding (PPB):  90.27074432373047%
Volume Distribution (VD):  0.591
Pgp-substrate:  5.035892486572266%

ADMET: Metabolism

CYP1A2-inhibitor:  0.979
CYP1A2-substrate:  0.811
CYP2C19-inhibitor:  0.916
CYP2C19-substrate:  0.105
CYP2C9-inhibitor:  0.833
CYP2C9-substrate:  0.937
CYP2D6-inhibitor:  0.935
CYP2D6-substrate:  0.859
CYP3A4-inhibitor:  0.696
CYP3A4-substrate:  0.223

ADMET: Excretion

Clearance (CL):  12.867
Half-life (T1/2):  0.856

ADMET: Toxicity

hERG Blockers:  0.065
Human Hepatotoxicity (H-HT):  0.071
Drug-inuced Liver Injury (DILI):  0.535
AMES Toxicity:  0.509
Rat Oral Acute Toxicity:  0.224
Maximum Recommended Daily Dose:  0.456
Skin Sensitization:  0.906
Carcinogencity:  0.209
Eye Corrosion:  0.009
Eye Irritation:  0.962
Respiratory Toxicity:  0.25

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

  Natural Product: NPC14063

Natural Product ID:  NPC14063
Common Name*:   FYPYWIYWMVCNCS-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FYPYWIYWMVCNCS-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H16O4/c1-20-15-10-12(17)9-14(19)16(15)13(18)8-7-11-5-3-2-4-6-11/h2-6,9-10,17,19H,7-8H2,1H3
SMILES:  COc1cc(cc(c1C(=O)CCc1ccccc1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6483649
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0003467] Linear 1,3-diarylpropanoids
        • [CHEMONTID:0001630] Chalcones and dihydrochalcones
          • [CHEMONTID:0003473] 2'-Hydroxy-dihydrochalcones

*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
NPO20502 Swertia cincta Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/cbdv.200490123]
NPO14915 Uvaria acuminata Species Annonaceae Eukaryota n.a. root n.a. PMID[14709883]
NPO7058 Australostichopus mollis Species Stichopodidae Eukaryota n.a. n.a. n.a. PMID[15974605]
NPO7058 Australostichopus mollis Species Stichopodidae Eukaryota n.a. n.a. n.a. PMID[22271309]
NPO40206 Monanthotaxis trichocarpa Species Annonaceae Eukaryota Roots n.a. n.a. PMID[31986029]
NPO21331 Syzygium samarangense Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20502 Swertia cincta Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14915 Uvaria acuminata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16941 Uvaria angolensis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21331 Syzygium samarangense Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20502 Swertia cincta Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16941 Uvaria angolensis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14915 Uvaria acuminata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16941 Uvaria angolensis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25162 Astragalus eupeplus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23099 Astragalus microcephalus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12116 Anabasis brevifolia Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17816 Parmelia latissima Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14915 Uvaria acuminata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18174 Rinodina lepida Species Physciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19209 Trichodesma zeylanicum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20363 Senecio morrisonensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16941 Uvaria angolensis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22878 Libocedrus bidwillii Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19790 Cyclamen africanum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15901 Pentanema indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8708 Vibrio cholerae Species Vibrionaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17722 Athroisma gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20502 Swertia cincta Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21331 Syzygium samarangense Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7058 Australostichopus mollis Species Stichopodidae 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 NPC14063 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 NPC14063 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