Structure

Physi-Chem Properties

Molecular Weight:  289.24
Volume:  337.865
LogP:  3.998
LogD:  3.657
LogS:  -3.583
# Rotatable Bonds:  10
TPSA:  20.31
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.331
Synthetic Accessibility Score:  2.656
Fsp3:  0.632
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:  -4.68
MDCK Permeability:  2.3338348910328932e-05
Pgp-inhibitor:  0.213
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.027
20% Bioavailability (F20%):  0.96
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.994
Plasma Protein Binding (PPB):  95.79639434814453%
Volume Distribution (VD):  0.907
Pgp-substrate:  4.10172700881958%

ADMET: Metabolism

CYP1A2-inhibitor:  0.478
CYP1A2-substrate:  0.837
CYP2C19-inhibitor:  0.501
CYP2C19-substrate:  0.616
CYP2C9-inhibitor:  0.45
CYP2C9-substrate:  0.722
CYP2D6-inhibitor:  0.285
CYP2D6-substrate:  0.858
CYP3A4-inhibitor:  0.898
CYP3A4-substrate:  0.225

ADMET: Excretion

Clearance (CL):  5.482
Half-life (T1/2):  0.815

ADMET: Toxicity

hERG Blockers:  0.183
Human Hepatotoxicity (H-HT):  0.653
Drug-inuced Liver Injury (DILI):  0.015
AMES Toxicity:  0.097
Rat Oral Acute Toxicity:  0.235
Maximum Recommended Daily Dose:  0.564
Skin Sensitization:  0.985
Carcinogencity:  0.747
Eye Corrosion:  0.081
Eye Irritation:  0.314
Respiratory Toxicity:  0.922

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General Info & Identifiers & Properties  
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Similar NPs/Drugs  

  Natural Product: NPC42477

Natural Product ID:  NPC42477
Common Name*:   1-[(2E,4E,8Z)-Tetradecatrienoyl]Piperidine
IUPAC Name:   (2E,4E,8Z)-1-piperidin-1-yltetradeca-2,4,8-trien-1-one
Synonyms:  
Standard InCHIKey:  DHGGORSOUREXQR-INAOPUJYSA-N
Standard InCHI:  InChI=1S/C19H31NO/c1-2-3-4-5-6-7-8-9-10-11-13-16-19(21)20-17-14-12-15-18-20/h6-7,10-11,13,16H,2-5,8-9,12,14-15,17-18H2,1H3/b7-6-,11-10+,16-13+
SMILES:  CCCCC/C=CCC/C=C/C=C/C(=O)N1CCCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2442643
PubChem CID:   11173777
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000195] Piperidines
        • [CHEMONTID:0000335] N-acylpiperidines

*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
NPO14864 Clerodendrum cyrtophyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[11473423]
NPO10210 Artabotrys uncinatus Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11575948]
NPO12347 Pseudomonas syringae Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[14714872]
NPO15548 Sinularia leptoclados Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[16724859]
NPO10210 Artabotrys uncinatus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15166 Cephalotaxus hainanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12993 Polypodium vulgare Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12993 Polypodium vulgare Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9734 Vincetoxicum hirundinaria Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15166 Cephalotaxus hainanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7042 Myrica arborea Species Myricaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8392 Iryanthera polyneura Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10210 Artabotrys uncinatus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12993 Polypodium vulgare Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15166 Cephalotaxus hainanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4699 Dracaena ombet Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12347 Pseudomonas syringae Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8392 Iryanthera polyneura Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11151 Arnebia decumbens Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19872 Achillea magnifica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10210 Artabotrys uncinatus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9734 Vincetoxicum hirundinaria Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4503 Bryonopsis laciniosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14864 Clerodendrum cyrtophyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20070 Crinum stuhlmannii Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11683 Crotalaria mitchellii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12539 Lissoclinum japonicum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5469 Pseudoxandra sclerocarpa Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22084 Stypandra imbricata Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7042 Myrica arborea Species Myricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4518.1 Saccharothrix mutabilis subsp. capreolus Subspecies Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12993 Polypodium vulgare Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6367 Cortinarius viola Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15166 Cephalotaxus hainanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13549 Otanthus maritimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26712 Cladrastis kentukea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12121 Streptomyces naraensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO3974 Ferula gummosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14989 Acanthothamnus aphyllus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13320 Glycosmis puberula Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11505 Nigella aristata Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9338 Polygala aureocauda Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14191 Berkheya rhapontica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15066 Iridaea membranacea Species Gigartinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15548 Sinularia leptoclados Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1027 Scrophularia leucoclada Species Scrophulariaceae 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
NPT1167 Individual Protein Delta opioid receptor Mus musculus Ki = 3800.0 nM PMID[506209]
NPT1168 Individual Protein Mu opioid receptor Mus musculus Ki = 7400.0 nM PMID[506209]
NPT1169 Individual Protein Cannabinoid CB2 receptor Mus musculus Ki = 160.0 nM PMID[506209]
NPT1170 Individual Protein Cannabinoid CB1 receptor Mus musculus Ki = 800.0 nM PMID[506209]
NPT2 Others Unspecified Ratio Ki = 0.51 n.a. PMID[506209]
NPT2 Others Unspecified Ratio Ki = 5.0 n.a. PMID[506209]

☑ 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 NPC42477 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
0.9492 High Similarity NPC206660
0.8814 High Similarity NPC133923
0.8644 High Similarity NPC385
0.8525 High Similarity NPC252684
0.7857 Intermediate Similarity NPC34672
0.75 Intermediate Similarity NPC214125
0.75 Intermediate Similarity NPC320667
0.7361 Intermediate Similarity NPC63284
0.7333 Intermediate Similarity NPC209232
0.7246 Intermediate Similarity NPC96272
0.697 Remote Similarity NPC470738
0.6933 Remote Similarity NPC86452
0.6933 Remote Similarity NPC244256
0.6753 Remote Similarity NPC120699
0.6753 Remote Similarity NPC132858
0.6753 Remote Similarity NPC77890
0.6753 Remote Similarity NPC127430
0.6753 Remote Similarity NPC267203
0.675 Remote Similarity NPC234822
0.675 Remote Similarity NPC61321
0.675 Remote Similarity NPC78058
0.675 Remote Similarity NPC143344
0.675 Remote Similarity NPC135639
0.6618 Remote Similarity NPC477461
0.6618 Remote Similarity NPC477459
0.6582 Remote Similarity NPC226982
0.6582 Remote Similarity NPC277341
0.6543 Remote Similarity NPC475975
0.6533 Remote Similarity NPC470994
0.6528 Remote Similarity NPC23721
0.6506 Remote Similarity NPC305602
0.6506 Remote Similarity NPC17497
0.6341 Remote Similarity NPC207048
0.6329 Remote Similarity NPC471768
0.6282 Remote Similarity NPC308050
0.6164 Remote Similarity NPC76869
0.6164 Remote Similarity NPC477460
0.6133 Remote Similarity NPC97614
0.6104 Remote Similarity NPC470992
0.6104 Remote Similarity NPC470993
0.6076 Remote Similarity NPC25513
0.6026 Remote Similarity NPC281154
0.6 Remote Similarity NPC28529
0.5974 Remote Similarity NPC26932
0.5972 Remote Similarity NPC476559
0.5897 Remote Similarity NPC473588
0.5897 Remote Similarity NPC78562
0.5843 Remote Similarity NPC145707
0.5833 Remote Similarity NPC208936
0.5814 Remote Similarity NPC157479
0.5806 Remote Similarity NPC120203
0.5789 Remote Similarity NPC90782
0.5778 Remote Similarity NPC473661
0.5769 Remote Similarity NPC326126
0.5714 Remote Similarity NPC474974
0.5714 Remote Similarity NPC231129
0.5698 Remote Similarity NPC147513
0.5634 Remote Similarity NPC82919

  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 NPC42477 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
0.6753 Remote Similarity NPD529 Approved
0.6053 Remote Similarity NPD816 Approved
0.6053 Remote Similarity NPD815 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