Structure

Physi-Chem Properties

Molecular Weight:  275.13
Volume:  299.213
LogP:  3.314
LogD:  3.878
LogS:  -4.295
# Rotatable Bonds:  8
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.59
Synthetic Accessibility Score:  2.725
Fsp3:  0.312
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:  -4.346
MDCK Permeability:  6.126546213636175e-05
Pgp-inhibitor:  0.023
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.35
20% Bioavailability (F20%):  0.282
30% Bioavailability (F30%):  0.073

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.189
Plasma Protein Binding (PPB):  92.69640350341797%
Volume Distribution (VD):  0.582
Pgp-substrate:  6.793722629547119%

ADMET: Metabolism

CYP1A2-inhibitor:  0.884
CYP1A2-substrate:  0.155
CYP2C19-inhibitor:  0.944
CYP2C19-substrate:  0.274
CYP2C9-inhibitor:  0.853
CYP2C9-substrate:  0.995
CYP2D6-inhibitor:  0.918
CYP2D6-substrate:  0.929
CYP3A4-inhibitor:  0.878
CYP3A4-substrate:  0.139

ADMET: Excretion

Clearance (CL):  2.796
Half-life (T1/2):  0.124

ADMET: Toxicity

hERG Blockers:  0.307
Human Hepatotoxicity (H-HT):  0.476
Drug-inuced Liver Injury (DILI):  0.747
AMES Toxicity:  0.043
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.028
Skin Sensitization:  0.8
Carcinogencity:  0.274
Eye Corrosion:  0.092
Eye Irritation:  0.891
Respiratory Toxicity:  0.879

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC300455

Natural Product ID:  NPC300455
Common Name*:   (2E,4E,6E)-N-Isopentyl-7-(2-Thienyl)-2,4,6-Heptatrienamide
IUPAC Name:   (2E,4E,6E)-N-(3-methylbutyl)-7-thiophen-2-ylhepta-2,4,6-trienamide
Synonyms:  
Standard InCHIKey:  CDHCPJUXYQLWFD-IZMYCKBJSA-N
Standard InCHI:  InChI=1S/C16H21NOS/c1-14(2)11-12-17-16(18)10-6-4-3-5-8-15-9-7-13-19-15/h3-10,13-14H,11-12H2,1-2H3,(H,17,18)/b4-3+,8-5+,10-6+
SMILES:  CC(CCN=C(/C=C/C=C/C=C/c1cccs1)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2442635
PubChem CID:   72696080
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
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 = 26500.0 nM PMID[458184]
NPT1168 Individual Protein Mu opioid receptor Mus musculus Ki = 8100.0 nM PMID[458184]
NPT1169 Individual Protein Cannabinoid CB2 receptor Mus musculus Ki = 5000.0 nM PMID[458184]
NPT1170 Individual Protein Cannabinoid CB1 receptor Mus musculus Ki = 2200.0 nM PMID[458184]
NPT2 Others Unspecified Ratio Ki = 3.27 n.a. PMID[458184]
NPT2 Others Unspecified Ratio Ki = 0.44 n.a. PMID[458184]

☑ 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 NPC300455 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
0.9655 High Similarity NPC166487
0.8431 Intermediate Similarity NPC190955
0.7419 Intermediate Similarity NPC471376
0.6952 Remote Similarity NPC120203
0.6889 Remote Similarity NPC105991
0.6822 Remote Similarity NPC11466
0.6804 Remote Similarity NPC14326
0.6737 Remote Similarity NPC299367
0.6667 Remote Similarity NPC2751
0.663 Remote Similarity NPC470796
0.6471 Remote Similarity NPC473031
0.6436 Remote Similarity NPC3210
0.64 Remote Similarity NPC472169
0.6373 Remote Similarity NPC203076
0.6239 Remote Similarity NPC475013
0.6239 Remote Similarity NPC474934
0.6238 Remote Similarity NPC307163
0.617 Remote Similarity NPC470795
0.6162 Remote Similarity NPC8981
0.6161 Remote Similarity NPC173019
0.6134 Remote Similarity NPC476048
0.61 Remote Similarity NPC195713
0.6078 Remote Similarity NPC471895
0.6018 Remote Similarity NPC475115
0.5929 Remote Similarity NPC469457
0.5877 Remote Similarity NPC472171
0.5856 Remote Similarity NPC175376
0.5826 Remote Similarity NPC472172
0.5804 Remote Similarity NPC33168
0.5794 Remote Similarity NPC12429
0.5776 Remote Similarity NPC472170
0.5755 Remote Similarity NPC148231
0.5741 Remote Similarity NPC470877
0.5714 Remote Similarity NPC317400
0.5714 Remote Similarity NPC470794
0.5701 Remote Similarity NPC198747
0.5691 Remote Similarity NPC32356
0.5688 Remote Similarity NPC471307
0.5688 Remote Similarity NPC209764
0.5688 Remote Similarity NPC74936
0.5688 Remote Similarity NPC141139
0.5688 Remote Similarity NPC470797
0.5688 Remote Similarity NPC121872
0.5688 Remote Similarity NPC159178
0.5688 Remote Similarity NPC78041
0.5682 Remote Similarity NPC471992
0.5678 Remote Similarity NPC475086
0.5678 Remote Similarity NPC274089
0.5678 Remote Similarity NPC191215
0.5678 Remote Similarity NPC471447
0.5652 Remote Similarity NPC324077
0.5625 Remote Similarity NPC324702
0.5625 Remote Similarity NPC86966

  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 NPC300455 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
0.7568 Intermediate Similarity NPD3907 Clinical (unspecified phase)
0.7196 Intermediate Similarity NPD745 Clinical (unspecified phase)
0.717 Intermediate Similarity NPD793 Approved
0.713 Intermediate Similarity NPD183 Approved
0.7087 Intermediate Similarity NPD532 Approved
0.6975 Remote Similarity NPD5702 Clinical (unspecified phase)
0.6814 Remote Similarity NPD4991 Discontinued
0.6698 Remote Similarity NPD1672 Phase 2
0.6549 Remote Similarity NPD2242 Phase 1
0.6518 Remote Similarity NPD3459 Approved
0.6471 Remote Similarity NPD9356 Discontinued
0.6341 Remote Similarity NPD2389 Approved
0.6333 Remote Similarity NPD6360 Discontinued
0.627 Remote Similarity NPD4099 Approved
0.627 Remote Similarity NPD4100 Approved
0.6186 Remote Similarity NPD1105 Clinical (unspecified phase)
0.6167 Remote Similarity NPD1944 Phase 2
0.6132 Remote Similarity NPD4728 Approved
0.6068 Remote Similarity NPD5278 Discontinued
0.6034 Remote Similarity NPD445 Discontinued
0.6032 Remote Similarity NPD3356 Approved
0.6032 Remote Similarity NPD3355 Approved
0.6016 Remote Similarity NPD483 Approved
0.6015 Remote Similarity NPD2202 Clinical (unspecified phase)
0.5983 Remote Similarity NPD7156 Discontinued
0.5929 Remote Similarity NPD1979 Approved
0.5899 Remote Similarity NPD1978 Approved
0.5888 Remote Similarity NPD1628 Approved
0.5888 Remote Similarity NPD1629 Approved
0.587 Remote Similarity NPD2447 Discontinued
0.5868 Remote Similarity NPD2587 Approved
0.5856 Remote Similarity NPD3457 Approved
0.5856 Remote Similarity NPD3458 Approved
0.5856 Remote Similarity NPD3456 Approved
0.5827 Remote Similarity NPD3599 Approved
0.5827 Remote Similarity NPD4127 Clinical (unspecified phase)
0.582 Remote Similarity NPD2543 Discontinued
0.5806 Remote Similarity NPD1713 Approved
0.5802 Remote Similarity NPD2158 Clinical (unspecified phase)
0.5785 Remote Similarity NPD1265 Approved
0.5785 Remote Similarity NPD1267 Approved
0.5781 Remote Similarity NPD4273 Approved
0.576 Remote Similarity NPD430 Discontinued
0.5738 Remote Similarity NPD1280 Clinical (unspecified phase)
0.5714 Remote Similarity NPD446 Clinical (unspecified phase)
0.5714 Remote Similarity NPD838 Approved
0.5703 Remote Similarity NPD804 Clinical (unspecified phase)
0.5703 Remote Similarity NPD4480 Approved
0.5702 Remote Similarity NPD1796 Phase 3
0.5702 Remote Similarity NPD4008 Approved
0.5702 Remote Similarity NPD4007 Approved
0.5702 Remote Similarity NPD1067 Discontinued
0.5691 Remote Similarity NPD5589 Approved
0.5685 Remote Similarity NPD2019 Approved
0.5685 Remote Similarity NPD2018 Approved
0.5678 Remote Similarity NPD9702 Discontinued
0.5659 Remote Similarity NPD1877 Discontinued
0.5652 Remote Similarity NPD1795 Discontinued
0.5646 Remote Similarity NPD2020 Approved
0.563 Remote Similarity NPD4680 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