Structure

Physi-Chem Properties

Molecular Weight:  325.24
Volume:  387.763
LogP:  4.815
LogD:  4.566
LogS:  -4.468
# Rotatable Bonds:  11
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.438
Synthetic Accessibility Score:  3.545
Fsp3:  0.409
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.078
MDCK Permeability:  3.263676990172826e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.867

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.372
Plasma Protein Binding (PPB):  100.17040252685547%
Volume Distribution (VD):  0.731
Pgp-substrate:  1.5684435367584229%

ADMET: Metabolism

CYP1A2-inhibitor:  0.868
CYP1A2-substrate:  0.207
CYP2C19-inhibitor:  0.971
CYP2C19-substrate:  0.628
CYP2C9-inhibitor:  0.811
CYP2C9-substrate:  0.103
CYP2D6-inhibitor:  0.77
CYP2D6-substrate:  0.159
CYP3A4-inhibitor:  0.961
CYP3A4-substrate:  0.301

ADMET: Excretion

Clearance (CL):  8.001
Half-life (T1/2):  0.599

ADMET: Toxicity

hERG Blockers:  0.314
Human Hepatotoxicity (H-HT):  0.975
Drug-inuced Liver Injury (DILI):  0.94
AMES Toxicity:  0.437
Rat Oral Acute Toxicity:  0.719
Maximum Recommended Daily Dose:  0.933
Skin Sensitization:  0.974
Carcinogencity:  0.777
Eye Corrosion:  0.06
Eye Irritation:  0.618
Respiratory Toxicity:  0.945

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

  Natural Product: NPC119655

Natural Product ID:  NPC119655
Common Name*:   UZBWCKBPXRODJT-UFDOCAHHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  UZBWCKBPXRODJT-UFDOCAHHSA-N
Standard InCHI:  InChI=1S/C22H31NO/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-22(24)23-20-21(2)3/h6-7,10-13,16-19,21H,4-5,14-15,20H2,1-3H3,(H,23,24)/b7-6-,11-10-,13-12+,17-16+,19-18+
SMILES:  CCC/C=CC#C/C=CC=CCC/C=C/C=C/C(=NCC(C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3314941
PubChem CID:   NA
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
NPO18988 Lepidium meyenii Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[12932133]
NPO18988 Lepidium meyenii Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[23891163]
NPO18988 Lepidium meyenii Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[24972328]
NPO18553.1 Heliopsis helianthoides Under-species n.a. n.a. n.a. n.a. n.a. PMID[24972328]
NPO18553.1 Heliopsis helianthoides Under-species n.a. n.a. n.a. n.a. n.a. PMID[25479041]
NPO3631 Euphorbia boetica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[31507181]
NPO18988 Lepidium meyenii Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[33320645]
NPO15606 Smyrnium olusatrum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15606 Smyrnium olusatrum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18095 Siphocampylus macropodus Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22240 Microbulbifer variabilis Species Microbulbiferaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15418 Canavalia obtusifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16716 Gracilaria edulis Species Gracilariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18988 Lepidium meyenii Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17463 Geijera balansae Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15606 Smyrnium olusatrum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6745 Montanoa leucantha Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15775 Kielmeyera pumila Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3631 Euphorbia boetica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17854 Neobeguea mahafalensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15033 Emiliania huxleyi Species 0elaerhabdaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16935 Heliopsis buphthalmoides Species Asteraceae 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
NPT1287 Individual Protein Cannabinoid CB2 receptor Homo sapiens Ki = 9180.0 nM PMID[498303]
NPT232 Individual Protein Cannabinoid CB1 receptor Homo sapiens Ki = 8600.0 nM PMID[498303]
NPT2985 Individual Protein Monoglyceride lipase Mus musculus IC50 > 100000.0 nM PMID[498303]
NPT1418 Individual Protein Anandamide amidohydrolase Homo sapiens Efficacy = 84.0 % PMID[498303]
NPT1418 Individual Protein Anandamide amidohydrolase Homo sapiens IC50 = 17780.0 nM PMID[498303]
NPT466 Cell Line U-937 Homo sapiens Efficacy = 75.0 % PMID[498303]
NPT466 Cell Line U-937 Homo sapiens IC50 = 2450.0 nM PMID[498303]

☑ 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 NPC119655 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
0.98 High Similarity NPC167759
0.98 High Similarity NPC305288
0.98 High Similarity NPC56028
0.98 High Similarity NPC163912
0.9608 High Similarity NPC471991
0.9592 High Similarity NPC304223
0.9592 High Similarity NPC267340
0.9592 High Similarity NPC145032
0.9592 High Similarity NPC54542
0.9592 High Similarity NPC243539
0.9423 High Similarity NPC477049
0.9412 High Similarity NPC123669
0.9388 High Similarity NPC267692
0.9388 High Similarity NPC307435
0.9216 High Similarity NPC303672
0.902 High Similarity NPC195986
0.8868 High Similarity NPC471992
0.8868 High Similarity NPC297020
0.8868 High Similarity NPC273023
0.8704 High Similarity NPC261158
0.8704 High Similarity NPC104138
0.8704 High Similarity NPC24216
0.8704 High Similarity NPC306420
0.8679 High Similarity NPC246519
0.8679 High Similarity NPC124382
0.8679 High Similarity NPC13011
0.8679 High Similarity NPC14234
0.8679 High Similarity NPC184014
0.8679 High Similarity NPC44193
0.8679 High Similarity NPC269800
0.8679 High Similarity NPC132669
0.8103 Intermediate Similarity NPC6795
0.7931 Intermediate Similarity NPC312826
0.7895 Intermediate Similarity NPC245650
0.7885 Intermediate Similarity NPC91044
0.7541 Intermediate Similarity NPC471023
0.75 Intermediate Similarity NPC309877
0.746 Intermediate Similarity NPC187315
0.7419 Intermediate Similarity NPC235311
0.7419 Intermediate Similarity NPC253468
0.7333 Intermediate Similarity NPC150505
0.7333 Intermediate Similarity NPC74617
0.7302 Intermediate Similarity NPC477525
0.7258 Intermediate Similarity NPC77891
0.7188 Intermediate Similarity NPC315141
0.7188 Intermediate Similarity NPC129995
0.7119 Intermediate Similarity NPC4881
0.7115 Intermediate Similarity NPC470439
0.7115 Intermediate Similarity NPC86121
0.7097 Intermediate Similarity NPC324077
0.6935 Remote Similarity NPC130807
0.6866 Remote Similarity NPC471022
0.6825 Remote Similarity NPC273614
0.6613 Remote Similarity NPC210999
0.6604 Remote Similarity NPC206906
0.6571 Remote Similarity NPC314678
0.6562 Remote Similarity NPC29468
0.6545 Remote Similarity NPC299114
0.6462 Remote Similarity NPC182758
0.6429 Remote Similarity NPC180575
0.6393 Remote Similarity NPC242930
0.6364 Remote Similarity NPC138935
0.6232 Remote Similarity NPC249713
0.6102 Remote Similarity NPC328784
0.6102 Remote Similarity NPC291437
0.6094 Remote Similarity NPC321030
0.6094 Remote Similarity NPC325734
0.6026 Remote Similarity NPC14326
0.6 Remote Similarity NPC71053
0.6 Remote Similarity NPC325550
0.6 Remote Similarity NPC59408
0.6 Remote Similarity NPC304151
0.6 Remote Similarity NPC329003
0.6 Remote Similarity NPC326524
0.5965 Remote Similarity NPC269074
0.5915 Remote Similarity NPC45060
0.5915 Remote Similarity NPC280065
0.5915 Remote Similarity NPC291196
0.5915 Remote Similarity NPC103712
0.5902 Remote Similarity NPC208638
0.5844 Remote Similarity NPC314854
0.5844 Remote Similarity NPC313911
0.5818 Remote Similarity NPC269823
0.5806 Remote Similarity NPC61177
0.5741 Remote Similarity NPC103213
0.5741 Remote Similarity NPC182840
0.5741 Remote Similarity NPC255042
0.5741 Remote Similarity NPC29091
0.5741 Remote Similarity NPC15934
0.5738 Remote Similarity NPC261571
0.5735 Remote Similarity NPC477106
0.5735 Remote Similarity NPC316674
0.5714 Remote Similarity NPC256766
0.5714 Remote Similarity NPC213538
0.5714 Remote Similarity NPC110732
0.569 Remote Similarity NPC276825
0.5667 Remote Similarity NPC153538
0.5667 Remote Similarity NPC85079
0.5667 Remote Similarity NPC31194
0.5667 Remote Similarity NPC248884
0.5645 Remote Similarity NPC49494
0.5645 Remote Similarity NPC188341
0.5636 Remote Similarity NPC145077
0.5636 Remote Similarity NPC56917
0.5625 Remote Similarity NPC474644
0.5614 Remote Similarity NPC116934
0.561 Remote Similarity NPC3210
0.56 Remote Similarity NPC288086

  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 NPC119655 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
0.625 Remote Similarity NPD860 Phase 2
0.5932 Remote Similarity NPD4220 Pre-registration

  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