Structure

Physi-Chem Properties

Molecular Weight:  271.1
Volume:  288.02
LogP:  3.063
LogD:  3.656
LogS:  -4.43
# Rotatable Bonds:  5
TPSA:  20.31
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.598
Synthetic Accessibility Score:  3.376
Fsp3:  0.188
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.573
MDCK Permeability:  3.827996988547966e-05
Pgp-inhibitor:  0.155
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.365
20% Bioavailability (F20%):  0.887
30% Bioavailability (F30%):  0.941

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.158
Plasma Protein Binding (PPB):  90.66632080078125%
Volume Distribution (VD):  0.417
Pgp-substrate:  9.218548774719238%

ADMET: Metabolism

CYP1A2-inhibitor:  0.696
CYP1A2-substrate:  0.438
CYP2C19-inhibitor:  0.943
CYP2C19-substrate:  0.118
CYP2C9-inhibitor:  0.75
CYP2C9-substrate:  0.99
CYP2D6-inhibitor:  0.949
CYP2D6-substrate:  0.947
CYP3A4-inhibitor:  0.896
CYP3A4-substrate:  0.144

ADMET: Excretion

Clearance (CL):  1.611
Half-life (T1/2):  0.197

ADMET: Toxicity

hERG Blockers:  0.808
Human Hepatotoxicity (H-HT):  0.684
Drug-inuced Liver Injury (DILI):  0.362
AMES Toxicity:  0.057
Rat Oral Acute Toxicity:  0.048
Maximum Recommended Daily Dose:  0.13
Skin Sensitization:  0.957
Carcinogencity:  0.298
Eye Corrosion:  0.413
Eye Irritation:  0.961
Respiratory Toxicity:  0.935

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  Natural Product: NPC11466

Natural Product ID:  NPC11466
Common Name*:   1-[(2E,4E,6E)-7-(2-Thienyl)-2,4,6-Heptatrienoyl]-2,3-Dehydropiperidine
IUPAC Name:   (2E,4E,6E)-1-(3,4-dihydro-2H-pyridin-1-yl)-7-thiophen-2-ylhepta-2,4,6-trien-1-one
Synonyms:  
Standard InCHIKey:  PQZFVGYQXOZIIR-DEVQJBAHSA-N
Standard InCHI:  InChI=1S/C16H17NOS/c18-16(17-12-6-3-7-13-17)11-5-2-1-4-9-15-10-8-14-19-15/h1-2,4-6,8-12,14H,3,7,13H2/b2-1+,9-4+,11-5+
SMILES:  C(=CC=CC(=O)N1C=CCCC1)/C=C/c1cccs1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2442638
PubChem CID:   73346583
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000089] Pyridines and derivatives
        • [CHEMONTID:0002224] Hydropyridines
          • [CHEMONTID:0001934] Tetrahydropyridines

*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]
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[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]
NPO10210 Artabotrys uncinatus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19872 Achillea magnifica Species Asteraceae 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]
NPO9734 Vincetoxicum hirundinaria Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20070 Crinum stuhlmannii Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14864 Clerodendrum cyrtophyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12539 Lissoclinum japonicum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11683 Crotalaria mitchellii Species Fabaceae 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]
NPO12993 Polypodium vulgare Species Polypodiaceae 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]
NPO15166 Cephalotaxus hainanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6367 Cortinarius viola Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13549 Otanthus maritimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12121 Streptomyces naraensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO26712 Cladrastis kentukea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14989 Acanthothamnus aphyllus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3974 Ferula gummosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11505 Nigella aristata Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13320 Glycosmis puberula Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15066 Iridaea membranacea Species Gigartinaceae 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]
NPO1027 Scrophularia leucoclada Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15548 Sinularia leptoclados Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12347 Pseudomonas syringae Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4699 Dracaena ombet Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11151 Arnebia decumbens Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8392 Iryanthera polyneura Species Myristicaceae 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 = 11500.0 nM PMID[548379]
NPT1168 Individual Protein Mu opioid receptor Mus musculus Ki = 29000.0 nM PMID[548379]
NPT1169 Individual Protein Cannabinoid CB2 receptor Mus musculus Ki = 13500.0 nM PMID[548379]
NPT1170 Individual Protein Cannabinoid CB1 receptor Mus musculus Ki > 50000.0 nM PMID[548379]
NPT2 Others Unspecified Ratio Ki = 0.4 n.a. PMID[548379]

☑ 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 NPC11466 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
0.9167 High Similarity NPC120203
0.6822 Remote Similarity NPC300455
0.6731 Remote Similarity NPC53492
0.6729 Remote Similarity NPC473661
0.6698 Remote Similarity NPC166487
0.6505 Remote Similarity NPC471895
0.6505 Remote Similarity NPC307163
0.6333 Remote Similarity NPC475013
0.6311 Remote Similarity NPC471376
0.6289 Remote Similarity NPC105991
0.6262 Remote Similarity NPC17497
0.6262 Remote Similarity NPC305602
0.623 Remote Similarity NPC476048
0.6224 Remote Similarity NPC470796
0.6216 Remote Similarity NPC474974
0.6167 Remote Similarity NPC190955
0.6132 Remote Similarity NPC470794
0.6106 Remote Similarity NPC175376
0.6091 Remote Similarity NPC470797
0.6018 Remote Similarity NPC256452
0.5913 Remote Similarity NPC472258
0.5905 Remote Similarity NPC475573
0.5905 Remote Similarity NPC475289
0.5865 Remote Similarity NPC299367
0.5847 Remote Similarity NPC24122
0.5833 Remote Similarity NPC143516
0.581 Remote Similarity NPC8981
0.58 Remote Similarity NPC470795
0.5785 Remote Similarity NPC474973
0.5785 Remote Similarity NPC130898
0.5785 Remote Similarity NPC474804
0.5755 Remote Similarity NPC195713
0.5741 Remote Similarity NPC474088
0.5691 Remote Similarity NPC473676
0.5656 Remote Similarity NPC471447
0.5641 Remote Similarity NPC475920

  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 NPC11466 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
0.7009 Intermediate Similarity NPD532 Approved
0.6944 Remote Similarity NPD1672 Phase 2
0.6786 Remote Similarity NPD793 Approved
0.6522 Remote Similarity NPD745 Clinical (unspecified phase)
0.6508 Remote Similarity NPD3355 Approved
0.6508 Remote Similarity NPD3356 Approved
0.65 Remote Similarity NPD2587 Approved
0.6496 Remote Similarity NPD2242 Phase 1
0.6475 Remote Similarity NPD3907 Clinical (unspecified phase)
0.6466 Remote Similarity NPD5260 Approved
0.6466 Remote Similarity NPD183 Approved
0.6466 Remote Similarity NPD3459 Approved
0.6466 Remote Similarity NPD5258 Approved
0.6316 Remote Similarity NPD4680 Discontinued
0.629 Remote Similarity NPD1713 Approved
0.629 Remote Similarity NPD9356 Discontinued
0.6259 Remote Similarity NPD3388 Phase 1
0.6241 Remote Similarity NPD1979 Approved
0.6214 Remote Similarity NPD1978 Approved
0.6172 Remote Similarity NPD4478 Clinical (unspecified phase)
0.6131 Remote Similarity NPD2576 Suspended
0.6121 Remote Similarity NPD708 Approved
0.6118 Remote Similarity NPD2413 Phase 2
0.6107 Remote Similarity NPD4100 Approved
0.6107 Remote Similarity NPD4099 Approved
0.6102 Remote Similarity NPD1576 Approved
0.6016 Remote Similarity NPD1265 Approved
0.6016 Remote Similarity NPD1267 Approved
0.5986 Remote Similarity NPD2018 Approved
0.5986 Remote Similarity NPD2019 Approved
0.5946 Remote Similarity NPD2020 Approved
0.5942 Remote Similarity NPD5004 Approved
0.5923 Remote Similarity NPD2439 Approved
0.5902 Remote Similarity NPD4063 Clinical (unspecified phase)
0.5844 Remote Similarity NPD2966 Clinical (unspecified phase)
0.584 Remote Similarity NPD5064 Approved
0.584 Remote Similarity NPD5063 Approved
0.5806 Remote Similarity NPD4991 Discontinued
0.5804 Remote Similarity NPD4728 Approved
0.576 Remote Similarity NPD1105 Clinical (unspecified phase)
0.5738 Remote Similarity NPD445 Discontinued
0.5735 Remote Similarity NPD6729 Phase 2
0.5695 Remote Similarity NPD1999 Phase 3
0.5695 Remote Similarity NPD2000 Phase 3
0.5692 Remote Similarity NPD3466 Discontinued
0.569 Remote Similarity NPD3457 Approved
0.569 Remote Similarity NPD3456 Approved
0.569 Remote Similarity NPD3458 Approved
0.5678 Remote Similarity NPD784 Discontinued
0.5676 Remote Similarity NPD5638 Approved
0.5662 Remote Similarity NPD5442 Approved
0.5662 Remote Similarity NPD2158 Clinical (unspecified phase)
0.5656 Remote Similarity NPD1064 Approved
0.5656 Remote Similarity NPD1065 Approved
0.5646 Remote Similarity NPD1939 Approved
0.5639 Remote Similarity NPD4232 Approved
0.5615 Remote Similarity NPD430 Discontinued

  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