Structure

Physi-Chem Properties

Molecular Weight:  295.18
Volume:  318.268
LogP:  -0.095
LogD:  0.019
LogS:  -0.946
# Rotatable Bonds:  11
TPSA:  83.47
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.601
Synthetic Accessibility Score:  2.92
Fsp3:  0.562
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:  -4.56
MDCK Permeability:  3.5937762731919065e-05
Pgp-inhibitor:  0.966
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.028
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.985
Plasma Protein Binding (PPB):  74.1310043334961%
Volume Distribution (VD):  0.452
Pgp-substrate:  31.571027755737305%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.079
CYP2C19-inhibitor:  0.049
CYP2C19-substrate:  0.103
CYP2C9-inhibitor:  0.063
CYP2C9-substrate:  0.267
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.127
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.274

ADMET: Excretion

Clearance (CL):  4.795
Half-life (T1/2):  0.819

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.502
Drug-inuced Liver Injury (DILI):  0.042
AMES Toxicity:  0.081
Rat Oral Acute Toxicity:  0.031
Maximum Recommended Daily Dose:  0.876
Skin Sensitization:  0.965
Carcinogencity:  0.937
Eye Corrosion:  0.013
Eye Irritation:  0.153
Respiratory Toxicity:  0.887

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  Natural Product: NPC75428

Natural Product ID:  NPC75428
Common Name*:   VCRNTFWOWYDPLY-BHPBWERZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VCRNTFWOWYDPLY-BHPBWERZSA-N
Standard InCHI:  InChI=1S/C16H25NO4/c1-13(18)8-4-5-9-14(19)10-6-7-11-15(20)17-12-16(2,3)21/h4-5,7-9,11,14,19,21H,6,10,12H2,1-3H3,(H,17,20)/b8-4+,9-5+,11-7+/t14-/m0/s1
SMILES:  CC(=O)/C=C/C=C/[C@@H](CC/C=C/C(=NCC(C)(C)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   101357058
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000331] Fatty amides
          • [CHEMONTID:0001096] N-acyl amines

*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
NPO5852 Litsea glutinosa Species Lauraceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(00)88469-1]
NPO5852 Litsea glutinosa Species Lauraceae Eukaryota n.a. stem n.a. DOI[10.1016/S0031-9422(00)88469-1]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[24175626]
NPO12970 Aspergillus fischeri Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[31920082]
NPO10128 Aplysia punctata Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[9213585]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1070 Matricaria suffruticosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2892 Wikstroemia chamaedaphne Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8642 Lithospermum officinale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8471 Angelica taiwaniana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4120 Ulmus americana Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5852 Litsea glutinosa Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9087 Sarcococca vagans Species Buxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6320 Echinosophora koreensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2892 Wikstroemia chamaedaphne Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1070 Matricaria suffruticosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8642 Lithospermum officinale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8471 Angelica taiwaniana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5852 Litsea glutinosa Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9087 Sarcococca vagans Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6320 Echinosophora koreensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26898 Jacobaea vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4120 Ulmus americana Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9087 Sarcococca vagans Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8642 Lithospermum officinale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1070 Matricaria suffruticosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16266 Didymium bahiense Species Didymiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9476 Metapenaeus bennettae Species Penaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14793 Erica glauca Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO777 Kielmeyera coriacea Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9590 Xanthoria aureola Species Teloschistaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20059.1 Lactobacillus delbrueckii subsp. bulgaricus Subspecies Lactobacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2199 Tecoma pentaphylla Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3341 Leishmania major Species Trypanosomatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7028 Sida veronicaefolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10128 Aplysia punctata Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9995 Cynara humilis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13438 Centaurea calcitrapa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10264 Platonia insignis Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5604 Chelonia japonica Species Cheloniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1682 Rhytidoponera metallica Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6801 Bellium bellidioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6320 Echinosophora koreensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7650 Salvia munzii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12970 Aspergillus fischeri Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2015 Udotea petiolata Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15558 Leucas neufliseana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8642 Lithospermum officinale Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2999 Coprinellus flocculosus Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4523 Reaumuria hirtella Species Tamaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24083.1 Melanelixia fuliginosa subsp. glabratula Subspecies Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7841 Solanum transcaucasicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9733 Spongia bilamellata Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8022 Consolida hohenackeri Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6378 Wilcoxia viperina n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO8471 Angelica taiwaniana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26898 Jacobaea vulgaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6556 Garcinia intermedia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6894 Elegia deusta Species Restionaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5852 Litsea glutinosa Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1467 Wedelia prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7847 Senecio densiflorus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4120 Ulmus americana Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9087 Sarcococca vagans Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2892 Wikstroemia chamaedaphne Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9221 Trachelospermum lucidum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8253 Alexandrium hiranoi Species Gonyaulacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4895 Coleus esquirolii Species Lamiaceae 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 NPC75428 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 NPC75428 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