Structure

Physi-Chem Properties

Molecular Weight:  221.18
Volume:  254.021
LogP:  3.13
LogD:  2.803
LogS:  -2.65
# Rotatable Bonds:  7
TPSA:  20.31
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.498
Synthetic Accessibility Score:  2.519
Fsp3:  0.643
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:  -4.586
MDCK Permeability:  2.067211244138889e-05
Pgp-inhibitor:  0.243
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.068
30% Bioavailability (F30%):  0.124

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.985
Plasma Protein Binding (PPB):  89.3485336303711%
Volume Distribution (VD):  0.832
Pgp-substrate:  12.709161758422852%

ADMET: Metabolism

CYP1A2-inhibitor:  0.266
CYP1A2-substrate:  0.767
CYP2C19-inhibitor:  0.333
CYP2C19-substrate:  0.785
CYP2C9-inhibitor:  0.249
CYP2C9-substrate:  0.485
CYP2D6-inhibitor:  0.06
CYP2D6-substrate:  0.488
CYP3A4-inhibitor:  0.452
CYP3A4-substrate:  0.282

ADMET: Excretion

Clearance (CL):  7.145
Half-life (T1/2):  0.482

ADMET: Toxicity

hERG Blockers:  0.09
Human Hepatotoxicity (H-HT):  0.576
Drug-inuced Liver Injury (DILI):  0.018
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.562
Maximum Recommended Daily Dose:  0.74
Skin Sensitization:  0.978
Carcinogencity:  0.558
Eye Corrosion:  0.324
Eye Irritation:  0.685
Respiratory Toxicity:  0.916

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General Info & Identifiers & Properties  
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Similar NPs/Drugs  

  Natural Product: NPC385

Natural Product ID:  NPC385
Common Name*:   Sarmentine
IUPAC Name:   (2E,4E)-1-pyrrolidin-1-yldeca-2,4-dien-1-one
Synonyms:   Sarmentine
Standard InCHIKey:  BFZBGTMIBOQWBA-HRCSPUOPSA-N
Standard InCHI:  InChI=1S/C14H23NO/c1-2-3-4-5-6-7-8-11-14(16)15-12-9-10-13-15/h6-8,11H,2-5,9-10,12-13H2,1H3/b7-6+,11-8+
SMILES:  CCCCC/C=C/C=C/C(=O)N1CCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2205104
PubChem CID:   6440616
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines
        • [CHEMONTID:0003023] N-acylpyrrolidines

*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
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. fruit n.a. DOI[10.1016/S0040-4039(01)00209-X]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[10575373]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. leaf n.a. PMID[15467205]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. whole plant n.a. PMID[16808005]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[16872768]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. whole plant n.a. PMID[17243725]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota whole plants Sendai, Miyagi Prefecture, Japan 2000-Sep PMID[17243725]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. whole plant n.a. PMID[17397219]
NPO26237 Piper longum Species Piperaceae Eukaryota fruits n.a. n.a. PMID[20839888]
NPO30128 Piper boehmeriaefolium Species Piperaceae Eukaryota whole plant Luxi County, Yunnan Province, China 2008-OCT PMID[21158422]
NPO30128 Piper boehmeriaefolium Species Piperaceae Eukaryota n.a. whole plant n.a. PMID[21158422]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. leaf n.a. PMID[21973101]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. inflorescence n.a. PMID[21973101]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota aerial parts Kego Nature Reserve, Hatinh Province, Vietnam 2008-DEC PMID[21973101]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. Kego Nature Reserve, Hatinh Province, Vietnam 2008-DEC PMID[21973101]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. twig n.a. PMID[21973101]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. stem n.a. PMID[21973101]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[22940450]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[23102654]
NPO4720 Aglaia perviridis Species Meliaceae Eukaryota leaves, twigs, and fruits Nui Chua National Park (11 43' N; 109 08' E; 730 m alt.), Ninh Thuan Province, Vietnam 2010-Jan PMID[23301897]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[23434420]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[31103896]
NPO4720 Aglaia perviridis Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[31621322]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28928 Piper nigrum Species Piperaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30128 Piper boehmeriaefolium Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5657 Oocystis polymorpha Species Oocystaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1912 Acanthosyris paulo-alvinii Species Cervantesiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO61 Phoebe grandis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4720 Aglaia perviridis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO992 Betula alnoides Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6614 Rubus pileatus Species Rosaceae 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
NPT116 Cell Line HL-60 Homo sapiens IC50 > 50000.0 nM PMID[511233]
NPT81 Cell Line A549 Homo sapiens IC50 > 40000.0 nM PMID[511235]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 40000.0 nM PMID[511235]
NPT133 Cell Line ZR-75-1 Homo sapiens IC50 > 40000.0 nM PMID[511235]
NPT134 Cell Line SK-BR-3 Homo sapiens IC50 > 40000.0 nM PMID[511235]
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 > 40000.0 nM PMID[511235]
NPT90 Cell Line DU-145 Homo sapiens IC50 > 40000.0 nM PMID[511235]
NPT91 Cell Line KB Homo sapiens IC50 > 40000.0 nM PMID[511235]
NPT115 Organism Mycobacterium tuberculosis H37Ra Mycobacterium tuberculosis H37Ra MIC = 50.0 ug.mL-1 PMID[511232]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 50000.0 nM PMID[511233]
NPT117 Organism Echinochloa crus-galli Echinochloa crus-galli mortality = 80.0 % PMID[511234]
NPT119 Organism Triticum aestivum Triticum aestivum mortality = 80.0 % PMID[511234]
NPT120 Organism Zea mays Zea mays mortality = 80.0 % PMID[511234]
NPT26740 ORGANISM Rumex crispus Rumex crispus mortality = 80.0 % PMID[511234]
NPT122 Organism Solanum nigrum Solanum nigrum mortality = 80.0 % PMID[511234]
NPT26742 ORGANISM Sinapis arvensis Sinapis arvensis mortality = 80.0 % PMID[511234]
NPT124 Organism Poa annua Poa annua mortality = 80.0 % PMID[511234]
NPT125 Organism Chenopodium album Chenopodium album mortality = 80.0 % PMID[511234]
NPT126 Organism Taraxacum officinale Taraxacum officinale mortality = 80.0 % PMID[511234]
NPT26744 ORGANISM Leptochloa Leptochloa mortality = 80.0 % PMID[511234]
NPT128 Organism Cyperus difformis Cyperus difformis mortality = 20.0 % PMID[511234]
NPT26745 ORGANISM Conyza canadensis Conyza canadensis mortality < 20.0 % PMID[511234]
NPT130 Organism Digitaria sanguinalis Digitaria sanguinalis mortality = 80.0 % PMID[511234]
NPT131 Organism Convolvulus arvensis Convolvulus arvensis mortality = 80.0 % PMID[511234]
NPT132 Organism Amaranthus retroflexus Amaranthus retroflexus mortality = 80.0 % PMID[511234]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 40000.0 nM PMID[511235]

☑ 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 NPC385 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
0.9818 High Similarity NPC133923
0.9474 High Similarity NPC252684
0.8644 High Similarity NPC42477
0.8226 Intermediate Similarity NPC206660
0.8 Intermediate Similarity NPC96272
0.72 Intermediate Similarity NPC277341
0.72 Intermediate Similarity NPC226982
0.6923 Remote Similarity NPC475975
0.6849 Remote Similarity NPC34672
0.6757 Remote Similarity NPC320667
0.6757 Remote Similarity NPC214125
0.6667 Remote Similarity NPC25513
0.6622 Remote Similarity NPC63284
0.6494 Remote Similarity NPC471768
0.6418 Remote Similarity NPC470738
0.641 Remote Similarity NPC209232
0.6234 Remote Similarity NPC86452
0.6234 Remote Similarity NPC244256
0.6207 Remote Similarity NPC474974
0.6164 Remote Similarity NPC90782
0.6133 Remote Similarity NPC326126
0.6098 Remote Similarity NPC234822
0.6098 Remote Similarity NPC61321
0.6098 Remote Similarity NPC135639
0.6098 Remote Similarity NPC143344
0.6098 Remote Similarity NPC78058
0.6081 Remote Similarity NPC97614
0.6076 Remote Similarity NPC120699
0.6076 Remote Similarity NPC127430
0.6076 Remote Similarity NPC77890
0.6076 Remote Similarity NPC267203
0.6076 Remote Similarity NPC132858
0.6034 Remote Similarity NPC208936
0.6026 Remote Similarity NPC46268
0.5946 Remote Similarity NPC477688
0.5921 Remote Similarity NPC252503
0.5882 Remote Similarity NPC17497
0.5882 Remote Similarity NPC305602
0.5857 Remote Similarity NPC477461
0.5857 Remote Similarity NPC477459
0.5789 Remote Similarity NPC217923
0.575 Remote Similarity NPC28529
0.5714 Remote Similarity NPC207048
0.569 Remote Similarity NPC323278
0.5663 Remote Similarity NPC473810
0.5647 Remote Similarity NPC76283
0.5641 Remote Similarity NPC470994
0.5625 Remote Similarity NPC308050
0.5614 Remote Similarity NPC234196
0.56 Remote Similarity NPC23721

  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 NPC385 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
0.6076 Remote Similarity NPD529 Approved
0.5789 Remote Similarity NPD815 Approved
0.5789 Remote Similarity NPD816 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