Structure

Physi-Chem Properties

Molecular Weight:  302.22
Volume:  356.238
LogP:  1.602
LogD:  2.584
LogS:  -2.929
# Rotatable Bonds:  13
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.335
Synthetic Accessibility Score:  3.037
Fsp3:  0.45
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -5.261
MDCK Permeability:  0.0001671500940574333
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.034
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.0
Plasma Protein Binding (PPB):  100.5973892211914%
Volume Distribution (VD):  0.39
Pgp-substrate:  0.5164121985435486%

ADMET: Metabolism

CYP1A2-inhibitor:  0.083
CYP1A2-substrate:  0.745
CYP2C19-inhibitor:  0.056
CYP2C19-substrate:  0.074
CYP2C9-inhibitor:  0.116
CYP2C9-substrate:  0.992
CYP2D6-inhibitor:  0.202
CYP2D6-substrate:  0.942
CYP3A4-inhibitor:  0.108
CYP3A4-substrate:  0.063

ADMET: Excretion

Clearance (CL):  2.276
Half-life (T1/2):  0.926

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.669
Drug-inuced Liver Injury (DILI):  0.003
AMES Toxicity:  0.83
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.677
Skin Sensitization:  0.962
Carcinogencity:  0.874
Eye Corrosion:  0.144
Eye Irritation:  0.407
Respiratory Toxicity:  0.923

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  Natural Product: NPC491246

Natural Product ID:  NPC491246
Common Name*:   Eicosapentaenoic Acid
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JAZBEHYOTPTENJ-IKHGVYGUSA-N
Standard InCHI:  InChI=1S/C20H30O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20(21)22/h3-4,6-7,9-10,12-13,15-16H,2,5,8,11,14,17-19H2,1H3,(H,21,22)/b4-3-,7-6-,10-9+,13-12-,16-15-
SMILES:  CCC=C/CC=C/CC=CCC=C/CC=C/CCCC(O)=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0002949] Long-chain fatty acids

*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
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-012-0441-5]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[1402962]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[17011103]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. PMID[24211545]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. n.a. PMID[26804051]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Flower Buds n.a. n.a. PMID[26977531]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO12323 Bos taurus Species Bovidae Eukaryota Urine n.a. n.a. PMID[6330305]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[8904847]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. PMID[932730]
NPO41172 Belone belone Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO19227 Hippoglossus hippoglossus Species Pleuronectidae Eukaryota n.a. n.a. Database[FooDB]
NPO41120 Nephrops norvegicus Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO27982 Brevoortia tyrannus Species Clupeidae Eukaryota n.a. n.a. Database[FooDB]
NPO41157 Sebastes alutus Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO41120 Nephrops norvegicus Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO41124 Oncorhynchus mykiss Species Salmonidae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO41127 Melanogrammus aeglefinus Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO41129 Anarhichas lupus Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO41167 Microstomus kitt Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO41157 Sebastes alutus Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO27982 Brevoortia tyrannus Species Clupeidae Eukaryota n.a. n.a. Database[FooDB]
NPO41170 Reinhardtius hippoglossoides Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO41167 Microstomus kitt Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO41127 Melanogrammus aeglefinus Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO41170 Reinhardtius hippoglossoides Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. Database[FooDB]
NPO41172 Belone belone Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO19227 Hippoglossus hippoglossus Species Pleuronectidae Eukaryota n.a. n.a. Database[FooDB]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO41129 Anarhichas lupus Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota Roots n.a. Database[FooDB]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. Database[FooDB]
NPO41124 Oncorhynchus mykiss Species Salmonidae Eukaryota n.a. n.a. Database[FooDB]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. Database[FooDB]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19227 Hippoglossus hippoglossus Species Pleuronectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27982 Brevoortia tyrannus Species Clupeidae 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
NPO12323 NPC491246 n.a. n.a. 48 n.a. n.a. mg/100g Database [FooDB]
NPO14821 NPC491246 n.a. n.a. 2 n.a. n.a. mg/100g Database [FooDB]
NPO14821 NPC491246 n.a. n.a. 4 n.a. n.a. mg/100g Database [FooDB]
NPO19227 NPC491246 n.a. n.a. 187 n.a. n.a. mg/100g Database [FooDB]
NPO27982 NPC491246 n.a. n.a. 13168 n.a. n.a. mg/100g Database [FooDB]
NPO3987 NPC491246 n.a. n.a. 9 n.a. n.a. mg/100g Database [FooDB]
NPO41120 NPC491246 n.a. n.a. 251 n.a. n.a. mg/100g Database [FooDB]
NPO41124 NPC491246 n.a. n.a. 322 n.a. n.a. mg/100g Database [FooDB]
NPO41127 NPC491246 n.a. n.a. 129 n.a. n.a. mg/100g Database [FooDB]
NPO41129 NPC491246 n.a. n.a. 451 n.a. n.a. mg/100g Database [FooDB]
NPO41157 NPC491246 n.a. n.a. 49 n.a. n.a. mg/100g Database [FooDB]
NPO41167 NPC491246 n.a. n.a. 247 n.a. n.a. mg/100g Database [FooDB]
NPO41170 NPC491246 n.a. n.a. 453 n.a. n.a. mg/100g Database [FooDB]
NPO41170 NPC491246 n.a. n.a. 1060 n.a. n.a. mg/100g Database [FooDB]
NPO41170 NPC491246 n.a. n.a. 1070 n.a. n.a. mg/100g Database [FooDB]
NPO41172 NPC491246 n.a. n.a. 143 n.a. n.a. mg/100g Database [FooDB]
NPO7576.2 NPC491246 n.a. n.a. 223 n.a. n.a. mg/100g Database [FooDB]

☑ 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

☑ 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 NPC491246 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

  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 NPC491246 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

  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