Structure

Physi-Chem Properties

Molecular Weight:  373.17
Volume:  398.0
LogP:  3.045
LogD:  3.579
LogS:  -4.069
# Rotatable Bonds:  13
TPSA:  55.4
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.204
Synthetic Accessibility Score:  3.054
Fsp3:  0.333
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:  -4.717
MDCK Permeability:  0.00010848033707588911
Pgp-inhibitor:  0.212
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.929
20% Bioavailability (F20%):  0.971
30% Bioavailability (F30%):  0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.02
Plasma Protein Binding (PPB):  92.83406066894531%
Volume Distribution (VD):  0.391
Pgp-substrate:  5.830417156219482%

ADMET: Metabolism

CYP1A2-inhibitor:  0.881
CYP1A2-substrate:  0.135
CYP2C19-inhibitor:  0.967
CYP2C19-substrate:  0.13
CYP2C9-inhibitor:  0.893
CYP2C9-substrate:  0.996
CYP2D6-inhibitor:  0.944
CYP2D6-substrate:  0.932
CYP3A4-inhibitor:  0.93
CYP3A4-substrate:  0.143

ADMET: Excretion

Clearance (CL):  3.724
Half-life (T1/2):  0.836

ADMET: Toxicity

hERG Blockers:  0.347
Human Hepatotoxicity (H-HT):  0.474
Drug-inuced Liver Injury (DILI):  0.894
AMES Toxicity:  0.41
Rat Oral Acute Toxicity:  0.035
Maximum Recommended Daily Dose:  0.053
Skin Sensitization:  0.925
Carcinogencity:  0.782
Eye Corrosion:  0.004
Eye Irritation:  0.046
Respiratory Toxicity:  0.786

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

  Natural Product: NPC190955

Natural Product ID:  NPC190955
Common Name*:   (2Z)-5-{[(2E,4E,6E)-7-(2-Thienyl)-2,4,6-Heptatrienoyl]Amino}-2-Pentenyl 3-Methylbutanoate
IUPAC Name:   [(Z)-5-[[(2E,4E,6E)-7-thiophen-2-ylhepta-2,4,6-trienoyl]amino]pent-2-enyl] 3-methylbutanoate
Synonyms:  
Standard InCHIKey:  UXKHBPOYZOPFIH-MKAYIHSVSA-N
Standard InCHI:  InChI=1S/C21H27NO3S/c1-18(2)17-21(24)25-15-9-5-8-14-22-20(23)13-7-4-3-6-11-19-12-10-16-26-19/h3-7,9-13,16,18H,8,14-15,17H2,1-2H3,(H,22,23)/b4-3+,9-5-,11-6+,13-7+
SMILES:  CC(C)CC(=O)OC/C=CCCN=C(/C=C/C=C/C=C/c1cccs1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2442639
PubChem CID:   72696081
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000324] Fatty acid esters

*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]
NPO7042 Myrica arborea Species Myricaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15166 Cephalotaxus hainanensis Species Taxaceae 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]
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]
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]
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]
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]

☑ 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 = 11000.0 nM PMID[534687]
NPT1168 Individual Protein Mu opioid receptor Mus musculus Ki = 41500.0 nM PMID[534687]
NPT1169 Individual Protein Cannabinoid CB2 receptor Mus musculus Ki = 10200.0 nM PMID[534687]
NPT1170 Individual Protein Cannabinoid CB1 receptor Mus musculus Ki = 5600.0 nM PMID[534687]
NPT2 Others Unspecified Ratio Ki = 0.27 n.a. PMID[534687]
NPT2 Others Unspecified Ratio Ki = 0.55 n.a. PMID[534687]

☑ 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 NPC190955 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
0.8431 Intermediate Similarity NPC300455
0.8317 Intermediate Similarity NPC166487
0.6967 Remote Similarity NPC32356
0.6723 Remote Similarity NPC475086
0.6449 Remote Similarity NPC471376
0.6283 Remote Similarity NPC2751
0.6271 Remote Similarity NPC120203
0.627 Remote Similarity NPC273814
0.6182 Remote Similarity NPC471895
0.6168 Remote Similarity NPC299367
0.6167 Remote Similarity NPC11466
0.6066 Remote Similarity NPC472172
0.605 Remote Similarity NPC474934
0.6048 Remote Similarity NPC274089
0.6048 Remote Similarity NPC191215
0.6036 Remote Similarity NPC472169
0.6036 Remote Similarity NPC307163
0.5984 Remote Similarity NPC472171
0.5982 Remote Similarity NPC470794
0.5962 Remote Similarity NPC105991
0.5952 Remote Similarity NPC182549
0.5952 Remote Similarity NPC114741
0.5946 Remote Similarity NPC14326
0.5926 Remote Similarity NPC160493
0.5896 Remote Similarity NPC80150
0.5896 Remote Similarity NPC476183
0.5859 Remote Similarity NPC323007
0.5854 Remote Similarity NPC173019
0.5852 Remote Similarity NPC476184
0.5852 Remote Similarity NPC476281
0.5814 Remote Similarity NPC475013
0.5812 Remote Similarity NPC470797
0.5793 Remote Similarity NPC477557
0.5789 Remote Similarity NPC3210
0.5778 Remote Similarity NPC190663
0.5766 Remote Similarity NPC476278
0.5755 Remote Similarity NPC470796
0.5726 Remote Similarity NPC475115
0.5725 Remote Similarity NPC476048
0.5725 Remote Similarity NPC476241
0.5725 Remote Similarity NPC476260
0.5702 Remote Similarity NPC175376
0.5683 Remote Similarity NPC476125
0.5683 Remote Similarity NPC476179
0.5678 Remote Similarity NPC185501
0.5669 Remote Similarity NPC471447
0.5658 Remote Similarity NPC283783
0.5645 Remote Similarity NPC469457
0.5635 Remote Similarity NPC472170
0.5629 Remote Similarity NPC474069
0.5612 Remote Similarity NPC475568
0.56 Remote Similarity NPC24122

  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 NPC190955 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
0.7456 Intermediate Similarity NPD183 Approved
0.7069 Intermediate Similarity NPD745 Clinical (unspecified phase)
0.6929 Remote Similarity NPD1979 Approved
0.6906 Remote Similarity NPD1978 Approved
0.6855 Remote Similarity NPD3907 Clinical (unspecified phase)
0.6667 Remote Similarity NPD4480 Approved
0.6591 Remote Similarity NPD4099 Approved
0.6591 Remote Similarity NPD4100 Approved
0.6562 Remote Similarity NPD3535 Clinical (unspecified phase)
0.6562 Remote Similarity NPD4209 Clinical (unspecified phase)
0.6557 Remote Similarity NPD5278 Discontinued
0.6531 Remote Similarity NPD2019 Approved
0.6531 Remote Similarity NPD2018 Approved
0.6486 Remote Similarity NPD2020 Approved
0.6434 Remote Similarity NPD446 Clinical (unspecified phase)
0.6364 Remote Similarity NPD1877 Discontinued
0.6364 Remote Similarity NPD5702 Clinical (unspecified phase)
0.6333 Remote Similarity NPD793 Approved
0.627 Remote Similarity NPD1279 Clinical (unspecified phase)
0.625 Remote Similarity NPD1116 Approved
0.625 Remote Similarity NPD1113 Approved
0.6241 Remote Similarity NPD4232 Approved
0.6239 Remote Similarity NPD532 Approved
0.622 Remote Similarity NPD1280 Clinical (unspecified phase)
0.619 Remote Similarity NPD4991 Discontinued
0.6154 Remote Similarity NPD1713 Approved
0.6099 Remote Similarity NPD2202 Clinical (unspecified phase)
0.6083 Remote Similarity NPD1067 Discontinued
0.6 Remote Similarity NPD5638 Approved
0.5985 Remote Similarity NPD6093 Discontinued
0.5972 Remote Similarity NPD5580 Discontinued
0.5962 Remote Similarity NPD3493 Approved
0.5962 Remote Similarity NPD3492 Approved
0.5962 Remote Similarity NPD3494 Approved
0.5946 Remote Similarity NPD2055 Phase 3
0.5946 Remote Similarity NPD2054 Approved
0.5944 Remote Similarity NPD1646 Approved
0.594 Remote Similarity NPD1245 Approved
0.5931 Remote Similarity NPD2862 Discontinued
0.5923 Remote Similarity NPD1246 Approved
0.5899 Remote Similarity NPD2158 Clinical (unspecified phase)
0.5894 Remote Similarity NPD6390 Discontinued
0.5891 Remote Similarity NPD5277 Phase 2
0.5882 Remote Similarity NPD6624 Discontinued
0.5874 Remote Similarity NPD1644 Approved
0.5874 Remote Similarity NPD1645 Phase 1
0.5857 Remote Similarity NPD4125 Approved
0.5839 Remote Similarity NPD6332 Clinical (unspecified phase)
0.5822 Remote Similarity NPD7137 Phase 2
0.5802 Remote Similarity NPD2635 Clinical (unspecified phase)
0.5789 Remote Similarity NPD2347 Approved
0.5789 Remote Similarity NPD9356 Discontinued
0.5789 Remote Similarity NPD6360 Discontinued
0.5786 Remote Similarity NPD4006 Discontinued
0.5785 Remote Similarity NPD1672 Phase 2
0.5779 Remote Similarity NPD2052 Approved
0.5766 Remote Similarity NPD3356 Approved
0.5766 Remote Similarity NPD3355 Approved
0.5764 Remote Similarity NPD5260 Approved
0.5764 Remote Similarity NPD5258 Approved
0.5758 Remote Similarity NPD6598 Approved
0.5758 Remote Similarity NPD6597 Approved
0.5742 Remote Similarity NPD2053 Approved
0.5742 Remote Similarity NPD22 Approved
0.5705 Remote Similarity NPD2513 Approved
0.5704 Remote Similarity NPD2045 Approved
0.5704 Remote Similarity NPD2046 Approved
0.5704 Remote Similarity NPD2043 Approved
0.5704 Remote Similarity NPD21 Approved
0.5704 Remote Similarity NPD2050 Clinical (unspecified phase)
0.5704 Remote Similarity NPD2051 Approved
0.5704 Remote Similarity NPD2049 Clinical (unspecified phase)
0.5704 Remote Similarity NPD2048 Approved
0.5704 Remote Similarity NPD2044 Approved
0.5704 Remote Similarity NPD2047 Approved
0.5703 Remote Similarity NPD2242 Phase 1
0.5683 Remote Similarity NPD5367 Discontinued
0.5677 Remote Similarity NPD2512 Phase 3
0.5669 Remote Similarity NPD3007 Approved
0.5669 Remote Similarity NPD3459 Approved
0.5669 Remote Similarity NPD2515 Approved
0.5664 Remote Similarity NPD5299 Approved
0.5646 Remote Similarity NPD6864 Phase 2
0.5646 Remote Similarity NPD6865 Phase 2
0.5646 Remote Similarity NPD3480 Approved
0.5639 Remote Similarity NPD1944 Phase 2
0.5633 Remote Similarity NPD5563 Clinical (unspecified phase)
0.5621 Remote Similarity NPD1971 Approved
0.5621 Remote Similarity NPD1970 Approved
0.5616 Remote Similarity NPD5004 Approved
0.561 Remote Similarity NPD5926 Approved
0.5603 Remote Similarity NPD6085 Phase 2
0.5603 Remote Similarity NPD5740 Clinical (unspecified phase)

  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