Structure

Physi-Chem Properties

Molecular Weight:  317.27
Volume:  378.377
LogP:  5.157
LogD:  4.819
LogS:  -4.615
# Rotatable Bonds:  14
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.262
Synthetic Accessibility Score:  3.54
Fsp3:  0.571
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:  -4.658
MDCK Permeability:  1.58784296218073e-05
Pgp-inhibitor:  0.02
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.018
20% Bioavailability (F20%):  0.303
30% Bioavailability (F30%):  0.424

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.078
Plasma Protein Binding (PPB):  99.8932876586914%
Volume Distribution (VD):  1.589
Pgp-substrate:  1.6048071384429932%

ADMET: Metabolism

CYP1A2-inhibitor:  0.576
CYP1A2-substrate:  0.385
CYP2C19-inhibitor:  0.715
CYP2C19-substrate:  0.521
CYP2C9-inhibitor:  0.619
CYP2C9-substrate:  0.818
CYP2D6-inhibitor:  0.668
CYP2D6-substrate:  0.877
CYP3A4-inhibitor:  0.851
CYP3A4-substrate:  0.133

ADMET: Excretion

Clearance (CL):  2.886
Half-life (T1/2):  0.87

ADMET: Toxicity

hERG Blockers:  0.671
Human Hepatotoxicity (H-HT):  0.863
Drug-inuced Liver Injury (DILI):  0.003
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.018
Maximum Recommended Daily Dose:  0.955
Skin Sensitization:  0.982
Carcinogencity:  0.193
Eye Corrosion:  0.03
Eye Irritation:  0.389
Respiratory Toxicity:  0.961

Download Data

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

  Natural Product: NPC471992

Natural Product ID:  NPC471992
Common Name*:   HGYPPGZPVQBDIS-UWKXONKZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HGYPPGZPVQBDIS-UWKXONKZSA-N
Standard InCHI:  InChI=1S/C21H35NO/c1-4-6-7-8-9-10-11-12-13-14-15-16-17-18-21(23)22-19-20(3)5-2/h7-8,10-11,15-18,20H,4-6,9,12-14,19H2,1-3H3,(H,22,23)/b8-7+,11-10+,16-15+,18-17+
SMILES:  CCC/C=C/C/C=C/CCC/C=C/C=C/C(=NCC(CC)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3314943
PubChem CID:   n.a.
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]
NPO18988 Lepidium meyenii Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[33320645]
NPO18988 Lepidium meyenii Species Brassicaceae 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 = 1210.0 nM PMID[522215]
NPT232 Individual Protein Cannabinoid CB1 receptor Homo sapiens Ki = 310.0 nM PMID[522215]
NPT2985 Individual Protein Monoglyceride lipase Mus musculus IC50 > 100000.0 nM PMID[522215]
NPT1418 Individual Protein Anandamide amidohydrolase Homo sapiens Efficacy = 80.0 % PMID[522215]
NPT1418 Individual Protein Anandamide amidohydrolase Homo sapiens IC50 = 19950.0 nM PMID[522215]
NPT466 Cell Line U-937 Homo sapiens IC50 = 2150.0 nM PMID[522215]
NPT466 Cell Line U-937 Homo sapiens Efficacy = 51.0 % PMID[522215]

☑ 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 NPC471992 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
0.9245 High Similarity NPC297020
0.9231 High Similarity NPC303672
0.9216 High Similarity NPC267340
0.9216 High Similarity NPC304223
0.9216 High Similarity NPC54542
0.9216 High Similarity NPC243539
0.9216 High Similarity NPC145032
0.9074 High Similarity NPC306420
0.9074 High Similarity NPC477049
0.9074 High Similarity NPC261158
0.9074 High Similarity NPC24216
0.9074 High Similarity NPC104138
0.9038 High Similarity NPC195986
0.902 High Similarity NPC267692
0.902 High Similarity NPC307435
0.8889 High Similarity NPC471991
0.8889 High Similarity NPC273023
0.8868 High Similarity NPC119655
0.8704 High Similarity NPC305288
0.8704 High Similarity NPC163912
0.8704 High Similarity NPC167759
0.8704 High Similarity NPC56028
0.8364 Intermediate Similarity NPC246519
0.8364 Intermediate Similarity NPC132669
0.8364 Intermediate Similarity NPC184014
0.8364 Intermediate Similarity NPC14234
0.8364 Intermediate Similarity NPC44193
0.8364 Intermediate Similarity NPC123669
0.8364 Intermediate Similarity NPC269800
0.8276 Intermediate Similarity NPC312826
0.8136 Intermediate Similarity NPC6795
0.8036 Intermediate Similarity NPC13011
0.8036 Intermediate Similarity NPC124382
0.7925 Intermediate Similarity NPC91044
0.7627 Intermediate Similarity NPC245650
0.7619 Intermediate Similarity NPC477525
0.7581 Intermediate Similarity NPC471023
0.75 Intermediate Similarity NPC315141
0.75 Intermediate Similarity NPC129995
0.75 Intermediate Similarity NPC187315
0.7458 Intermediate Similarity NPC4881
0.7258 Intermediate Similarity NPC309877
0.7258 Intermediate Similarity NPC130807
0.7213 Intermediate Similarity NPC210999
0.7188 Intermediate Similarity NPC253468
0.7188 Intermediate Similarity NPC235311
0.7143 Intermediate Similarity NPC324077
0.7097 Intermediate Similarity NPC150505
0.7097 Intermediate Similarity NPC74617
0.7031 Intermediate Similarity NPC77891
0.6912 Remote Similarity NPC471022
0.6875 Remote Similarity NPC29468
0.6857 Remote Similarity NPC314678
0.6852 Remote Similarity NPC470439
0.6852 Remote Similarity NPC86121
0.6727 Remote Similarity NPC138935
0.6721 Remote Similarity NPC242930
0.6615 Remote Similarity NPC273614
0.6522 Remote Similarity NPC249713
0.6515 Remote Similarity NPC182758
0.65 Remote Similarity NPC208638
0.6406 Remote Similarity NPC325734
0.6406 Remote Similarity NPC321030
0.6316 Remote Similarity NPC299114
0.6308 Remote Similarity NPC326524
0.6308 Remote Similarity NPC329003
0.6308 Remote Similarity NPC325550
0.6282 Remote Similarity NPC14326
0.6269 Remote Similarity NPC477106
0.6197 Remote Similarity NPC45060
0.6197 Remote Similarity NPC280065
0.6197 Remote Similarity NPC291196
0.6197 Remote Similarity NPC103712
0.6182 Remote Similarity NPC269823
0.6104 Remote Similarity NPC314854
0.6104 Remote Similarity NPC313911
0.6076 Remote Similarity NPC39966
0.6076 Remote Similarity NPC224072
0.6071 Remote Similarity NPC206906
0.6071 Remote Similarity NPC256766
0.6071 Remote Similarity NPC213538
0.6066 Remote Similarity NPC261571
0.6029 Remote Similarity NPC316674
0.6024 Remote Similarity NPC316186
0.5968 Remote Similarity NPC49494
0.5968 Remote Similarity NPC188341
0.5965 Remote Similarity NPC116934
0.5938 Remote Similarity NPC329686
0.5932 Remote Similarity NPC180575
0.5904 Remote Similarity NPC473031
0.5902 Remote Similarity NPC26960
0.5902 Remote Similarity NPC182102
0.5902 Remote Similarity NPC474460
0.5867 Remote Similarity NPC288086
0.5854 Remote Similarity NPC3210
0.5818 Remote Similarity NPC29091
0.5818 Remote Similarity NPC103213
0.5818 Remote Similarity NPC182840
0.5818 Remote Similarity NPC15934
0.5818 Remote Similarity NPC255042
0.5795 Remote Similarity NPC469739
0.5789 Remote Similarity NPC88079
0.5789 Remote Similarity NPC194586
0.5789 Remote Similarity NPC209279
0.5789 Remote Similarity NPC108494
0.5789 Remote Similarity NPC180871
0.5789 Remote Similarity NPC68889
0.5789 Remote Similarity NPC51758
0.5789 Remote Similarity NPC67761
0.5783 Remote Similarity NPC203076
0.5769 Remote Similarity NPC473695
0.5769 Remote Similarity NPC473446
0.5763 Remote Similarity NPC160628
0.5763 Remote Similarity NPC140501
0.575 Remote Similarity NPC184473
0.575 Remote Similarity NPC6902
0.575 Remote Similarity NPC284456
0.5735 Remote Similarity NPC176621
0.5714 Remote Similarity NPC56917
0.5692 Remote Similarity NPC474644
0.5682 Remote Similarity NPC300455
0.5667 Remote Similarity NPC308331
0.5663 Remote Similarity NPC152684
0.5645 Remote Similarity NPC328784
0.5645 Remote Similarity NPC291437
0.5625 Remote Similarity NPC476560
0.5618 Remote Similarity NPC50902
0.5618 Remote Similarity NPC233273
0.5618 Remote Similarity NPC205546
0.561 Remote Similarity NPC228638
0.5606 Remote Similarity NPC473865
0.5606 Remote Similarity NPC55412
0.5606 Remote Similarity NPC474643
0.5606 Remote Similarity NPC249645

  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 NPC471992 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
0.6034 Remote Similarity NPD860 Phase 2
0.6 Remote Similarity NPD4220 Pre-registration
0.5781 Remote Similarity NPD9652 Approved
0.5763 Remote Similarity NPD4265 Approved
0.5606 Remote Similarity NPD4219 Approved

  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