Structure

Physi-Chem Properties

Molecular Weight:  322.2
Volume:  360.087
LogP:  1.798
LogD:  2.783
LogS:  -3.022
# Rotatable Bonds:  14
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.325
Synthetic Accessibility Score:  3.11
Fsp3:  0.526
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:  -5.342
MDCK Permeability:  5.949544174654875e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.033
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.003
Plasma Protein Binding (PPB):  99.34778594970703%
Volume Distribution (VD):  0.577
Pgp-substrate:  0.7818627953529358%

ADMET: Metabolism

CYP1A2-inhibitor:  0.081
CYP1A2-substrate:  0.894
CYP2C19-inhibitor:  0.039
CYP2C19-substrate:  0.264
CYP2C9-inhibitor:  0.041
CYP2C9-substrate:  0.981
CYP2D6-inhibitor:  0.117
CYP2D6-substrate:  0.946
CYP3A4-inhibitor:  0.048
CYP3A4-substrate:  0.094

ADMET: Excretion

Clearance (CL):  3.143
Half-life (T1/2):  0.958

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.367
Drug-inuced Liver Injury (DILI):  0.008
AMES Toxicity:  0.932
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.293
Skin Sensitization:  0.943
Carcinogencity:  0.914
Eye Corrosion:  0.026
Eye Irritation:  0.24
Respiratory Toxicity:  0.743

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC477777

Natural Product ID:  NPC477777
Common Name*:   5-Thia-8,11,14,17-eicosatetraenoic acid
IUPAC Name:   4-[(3Z,6Z,9Z,12Z)-pentadeca-3,6,9,12-tetraenyl]sulfanylbutanoic acid
Synonyms:  
Standard InCHIKey:  JUGSAWFPXQSLMJ-LTKCOYKYSA-N
Standard InCHI:  InChI=1S/C19H30O2S/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-17-22-18-15-16-19(20)21/h3-4,6-7,9-10,12-13H,2,5,8,11,14-18H2,1H3,(H,20,21)/b4-3-,7-6-,10-9-,13-12-
SMILES:  CC/C=C\C/C=C\C/C=C\C/C=C\CCSCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10019057
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0001423] Thia 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
NPO21324 Plantago major Species Plantaginaceae Eukaryota Entire plants the surroundings of Uppsala, Sweden 1998-SEP PMID[11421736]
NPO21324 Plantago major Species Plantaginaceae Eukaryota Whole Plant the surroundings of Uppsala, Sweden 1998-SEP PMID[11421736]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. seed n.a. PMID[24895551]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[9784154]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21324 Plantago major Species Plantaginaceae 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
NPT325 Individual Protein Cyclooxygenase-2 Ovis aries IC50 = 3900 nM PMID[11421736]
NPT1665 Individual Protein Cyclooxygenase-1 Bos taurus IC50 = 26000 nM PMID[11421736]
NPT2 Others Unspecified Ratio IC50 = 0.2 n.a. PMID[11421736]

☑ 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 NPC477777 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
0.9792 High Similarity NPC477779
0.9149 High Similarity NPC477776
0.7755 Intermediate Similarity NPC270796
0.7451 Intermediate Similarity NPC117572
0.717 Intermediate Similarity NPC91495
0.7037 Intermediate Similarity NPC149821
0.7037 Intermediate Similarity NPC5413
0.6981 Remote Similarity NPC42304
0.6909 Remote Similarity NPC59051
0.6852 Remote Similarity NPC207292
0.6786 Remote Similarity NPC284212
0.6786 Remote Similarity NPC48162
0.6667 Remote Similarity NPC92114
0.6552 Remote Similarity NPC1813
0.6552 Remote Similarity NPC321062
0.6552 Remote Similarity NPC294548
0.6552 Remote Similarity NPC36061
0.6552 Remote Similarity NPC139029
0.6552 Remote Similarity NPC70387
0.6491 Remote Similarity NPC28205
0.6491 Remote Similarity NPC178586
0.6441 Remote Similarity NPC25417
0.6441 Remote Similarity NPC290563
0.6441 Remote Similarity NPC424
0.6441 Remote Similarity NPC88966
0.6441 Remote Similarity NPC281972
0.6441 Remote Similarity NPC32467
0.6441 Remote Similarity NPC87564
0.6441 Remote Similarity NPC154245
0.6441 Remote Similarity NPC261831
0.6441 Remote Similarity NPC6095
0.6441 Remote Similarity NPC322461
0.6441 Remote Similarity NPC85813
0.6383 Remote Similarity NPC14778
0.6379 Remote Similarity NPC303765
0.6379 Remote Similarity NPC129458
0.6379 Remote Similarity NPC281245
0.6333 Remote Similarity NPC274290
0.6333 Remote Similarity NPC317548
0.6333 Remote Similarity NPC473863
0.6275 Remote Similarity NPC329545
0.6271 Remote Similarity NPC10081
0.6271 Remote Similarity NPC225066
0.623 Remote Similarity NPC18951
0.623 Remote Similarity NPC327388
0.623 Remote Similarity NPC325977
0.623 Remote Similarity NPC179764
0.623 Remote Similarity NPC187777
0.623 Remote Similarity NPC477201
0.6207 Remote Similarity NPC43053
0.6167 Remote Similarity NPC137538
0.6154 Remote Similarity NPC123357
0.6129 Remote Similarity NPC323498
0.6129 Remote Similarity NPC323436
0.6129 Remote Similarity NPC225929
0.6129 Remote Similarity NPC323597
0.6129 Remote Similarity NPC211752
0.6071 Remote Similarity NPC87137
0.6066 Remote Similarity NPC45626
0.6066 Remote Similarity NPC52264
0.6066 Remote Similarity NPC54766
0.6034 Remote Similarity NPC224227
0.6032 Remote Similarity NPC329819
0.6 Remote Similarity NPC145235
0.5938 Remote Similarity NPC322002
0.5938 Remote Similarity NPC329550
0.5938 Remote Similarity NPC274927
0.5938 Remote Similarity NPC322186
0.5938 Remote Similarity NPC106851
0.5938 Remote Similarity NPC329249
0.5932 Remote Similarity NPC262968
0.5926 Remote Similarity NPC187922
0.5902 Remote Similarity NPC474127
0.5862 Remote Similarity NPC163345
0.5862 Remote Similarity NPC477778
0.5849 Remote Similarity NPC8270
0.5846 Remote Similarity NPC321919
0.5846 Remote Similarity NPC122521
0.5846 Remote Similarity NPC235242
0.5846 Remote Similarity NPC243532
0.5846 Remote Similarity NPC81896
0.5846 Remote Similarity NPC174447
0.5846 Remote Similarity NPC328311
0.5846 Remote Similarity NPC251042
0.5846 Remote Similarity NPC327112
0.5806 Remote Similarity NPC67367
0.5789 Remote Similarity NPC308331
0.5781 Remote Similarity NPC267817
0.5769 Remote Similarity NPC226511
0.5763 Remote Similarity NPC225974
0.5763 Remote Similarity NPC221467
0.5758 Remote Similarity NPC201939
0.5758 Remote Similarity NPC320305
0.5758 Remote Similarity NPC328776
0.5758 Remote Similarity NPC321838
0.5758 Remote Similarity NPC40082
0.5741 Remote Similarity NPC221250
0.5738 Remote Similarity NPC284224
0.5738 Remote Similarity NPC139545
0.5738 Remote Similarity NPC39633
0.5738 Remote Similarity NPC309606
0.5714 Remote Similarity NPC304079
0.5714 Remote Similarity NPC82239
0.5714 Remote Similarity NPC6963
0.5692 Remote Similarity NPC318306
0.569 Remote Similarity NPC180534
0.5672 Remote Similarity NPC322457
0.5645 Remote Similarity NPC300121
0.5625 Remote Similarity NPC283502
0.5625 Remote Similarity NPC472445

  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 NPC477777 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
0.7755 Intermediate Similarity NPD5326 Phase 3
0.7451 Intermediate Similarity NPD4222 Approved
0.7451 Intermediate Similarity NPD39 Approved
0.7037 Intermediate Similarity NPD3173 Approved
0.6604 Remote Similarity NPD6097 Approved
0.6604 Remote Similarity NPD6096 Approved
0.6552 Remote Similarity NPD3172 Approved
0.6481 Remote Similarity NPD3174 Discontinued
0.6441 Remote Similarity NPD3194 Approved
0.6441 Remote Similarity NPD3195 Phase 2
0.6441 Remote Similarity NPD4266 Approved
0.6441 Remote Similarity NPD3196 Approved
0.625 Remote Similarity NPD5343 Approved
0.6032 Remote Similarity NPD6109 Phase 1
0.5932 Remote Similarity NPD28 Approved
0.5932 Remote Similarity NPD29 Approved
0.5902 Remote Similarity NPD539 Approved
0.5862 Remote Similarity NPD4220 Pre-registration
0.5846 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5818 Remote Similarity NPD9411 Phase 1
0.569 Remote Similarity NPD622 Approved
0.5667 Remote Similarity NPD6927 Phase 3
0.5663 Remote Similarity NPD5370 Suspended

  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