Structure

Physi-Chem Properties

Molecular Weight:  322.2
Volume:  360.087
LogP:  2.572
LogD:  3.281
LogS:  -3.254
# 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:  3.15
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:  -5.232
MDCK Permeability:  3.6065598578716163e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.028
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.003
Plasma Protein Binding (PPB):  100.21027374267578%
Volume Distribution (VD):  0.426
Pgp-substrate:  0.5343899726867676%

ADMET: Metabolism

CYP1A2-inhibitor:  0.117
CYP1A2-substrate:  0.83
CYP2C19-inhibitor:  0.06
CYP2C19-substrate:  0.197
CYP2C9-inhibitor:  0.059
CYP2C9-substrate:  0.987
CYP2D6-inhibitor:  0.312
CYP2D6-substrate:  0.939
CYP3A4-inhibitor:  0.139
CYP3A4-substrate:  0.075

ADMET: Excretion

Clearance (CL):  2.696
Half-life (T1/2):  0.946

ADMET: Toxicity

hERG Blockers:  0.032
Human Hepatotoxicity (H-HT):  0.66
Drug-inuced Liver Injury (DILI):  0.008
AMES Toxicity:  0.077
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.612
Skin Sensitization:  0.953
Carcinogencity:  0.894
Eye Corrosion:  0.08
Eye Irritation:  0.405
Respiratory Toxicity:  0.645

Download Data

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

  Natural Product: NPC477779

Natural Product ID:  NPC477779
Common Name*:   (7E,11Z,14Z,17Z)-5-Thia-7,11,14,17-icosatetraenoic acid
IUPAC Name:   4-[(2E,6Z,9Z,12Z)-pentadeca-2,6,9,12-tetraenyl]sulfanylbutanoic acid
Synonyms:  
Standard InCHIKey:  PFXIXAVMUKVROB-TWMAVKMASA-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/h3-4,6-7,9-10,13-14H,2,5,8,11-12,15-18H2,1H3,(H,20,21)/b4-3-,7-6-,10-9-,14-13+
SMILES:  CC/C=C\C/C=C\C/C=C\CC/C=C/CSCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   44559942
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
NPT1665 Individual Protein Cyclooxygenase-1 Bos taurus IC50 = 81000 nM PMID[11421736]
NPT325 Individual Protein Cyclooxygenase-2 Ovis aries IC50 = 120000 nM PMID[11421736]
NPT2 Others Unspecified Ratio IC50 = 1.4 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 NPC477779 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 NPC477777
0.8958 High Similarity NPC477776
0.7959 Intermediate Similarity NPC270796
0.7647 Intermediate Similarity NPC117572
0.7358 Intermediate Similarity NPC91495
0.7222 Intermediate Similarity NPC149821
0.7222 Intermediate Similarity NPC5413
0.7091 Intermediate Similarity NPC59051
0.7037 Intermediate Similarity NPC207292
0.6964 Remote Similarity NPC48162
0.6852 Remote Similarity NPC42304
0.6842 Remote Similarity NPC92114
0.6724 Remote Similarity NPC1813
0.6724 Remote Similarity NPC36061
0.6724 Remote Similarity NPC321062
0.6724 Remote Similarity NPC70387
0.6724 Remote Similarity NPC139029
0.6724 Remote Similarity NPC294548
0.6667 Remote Similarity NPC178586
0.6667 Remote Similarity NPC28205
0.6667 Remote Similarity NPC284212
0.661 Remote Similarity NPC88966
0.661 Remote Similarity NPC424
0.661 Remote Similarity NPC281972
0.661 Remote Similarity NPC154245
0.661 Remote Similarity NPC87564
0.661 Remote Similarity NPC6095
0.661 Remote Similarity NPC25417
0.661 Remote Similarity NPC32467
0.661 Remote Similarity NPC290563
0.661 Remote Similarity NPC322461
0.661 Remote Similarity NPC85813
0.661 Remote Similarity NPC261831
0.6552 Remote Similarity NPC303765
0.6552 Remote Similarity NPC129458
0.6552 Remote Similarity NPC281245
0.65 Remote Similarity NPC473863
0.65 Remote Similarity NPC274290
0.65 Remote Similarity NPC317548
0.6441 Remote Similarity NPC10081
0.6441 Remote Similarity NPC225066
0.6393 Remote Similarity NPC477201
0.6393 Remote Similarity NPC18951
0.6393 Remote Similarity NPC325977
0.6393 Remote Similarity NPC327388
0.6393 Remote Similarity NPC187777
0.6393 Remote Similarity NPC179764
0.6333 Remote Similarity NPC137538
0.629 Remote Similarity NPC225929
0.629 Remote Similarity NPC323597
0.629 Remote Similarity NPC211752
0.629 Remote Similarity NPC323436
0.629 Remote Similarity NPC323498
0.625 Remote Similarity NPC14778
0.623 Remote Similarity NPC54766
0.623 Remote Similarity NPC45626
0.623 Remote Similarity NPC52264
0.6207 Remote Similarity NPC224227
0.619 Remote Similarity NPC329819
0.6154 Remote Similarity NPC329545
0.6102 Remote Similarity NPC43053
0.6102 Remote Similarity NPC262968
0.6094 Remote Similarity NPC106851
0.6094 Remote Similarity NPC329550
0.6094 Remote Similarity NPC322186
0.6094 Remote Similarity NPC274927
0.6094 Remote Similarity NPC322002
0.6094 Remote Similarity NPC329249
0.6066 Remote Similarity NPC474127
0.6038 Remote Similarity NPC123357
0.6 Remote Similarity NPC81896
0.6 Remote Similarity NPC321919
0.6 Remote Similarity NPC243532
0.6 Remote Similarity NPC328311
0.6 Remote Similarity NPC327112
0.6 Remote Similarity NPC122521
0.6 Remote Similarity NPC235242
0.6 Remote Similarity NPC174447
0.6 Remote Similarity NPC251042
0.5968 Remote Similarity NPC67367
0.5965 Remote Similarity NPC87137
0.5965 Remote Similarity NPC308331
0.5938 Remote Similarity NPC267817
0.5932 Remote Similarity NPC225974
0.5926 Remote Similarity NPC221250
0.5909 Remote Similarity NPC328776
0.5909 Remote Similarity NPC201939
0.5909 Remote Similarity NPC40082
0.5909 Remote Similarity NPC320305
0.5909 Remote Similarity NPC321838
0.5902 Remote Similarity NPC39633
0.5902 Remote Similarity NPC139545
0.5902 Remote Similarity NPC145235
0.5902 Remote Similarity NPC309606
0.5902 Remote Similarity NPC284224
0.5893 Remote Similarity NPC304079
0.5893 Remote Similarity NPC6963
0.5862 Remote Similarity NPC180534
0.5846 Remote Similarity NPC318306
0.5821 Remote Similarity NPC322457
0.5818 Remote Similarity NPC187922
0.5806 Remote Similarity NPC300121
0.5781 Remote Similarity NPC472445
0.5781 Remote Similarity NPC283502
0.5763 Remote Similarity NPC267110
0.5763 Remote Similarity NPC477778
0.5763 Remote Similarity NPC163345
0.5763 Remote Similarity NPC135698
0.5763 Remote Similarity NPC207815
0.5741 Remote Similarity NPC8270
0.5738 Remote Similarity NPC18357
0.5738 Remote Similarity NPC151919
0.5735 Remote Similarity NPC476658
0.5735 Remote Similarity NPC328089
0.5735 Remote Similarity NPC68343
0.5735 Remote Similarity NPC470320
0.5714 Remote Similarity NPC474672
0.5714 Remote Similarity NPC28779
0.5714 Remote Similarity NPC319021
0.5714 Remote Similarity NPC128061
0.5714 Remote Similarity NPC223677
0.5714 Remote Similarity NPC228473
0.5714 Remote Similarity NPC200845
0.5714 Remote Similarity NPC477984
0.5714 Remote Similarity NPC10316
0.5692 Remote Similarity NPC471619
0.5692 Remote Similarity NPC325734
0.5692 Remote Similarity NPC254095
0.5692 Remote Similarity NPC34416
0.5672 Remote Similarity NPC125312
0.5672 Remote Similarity NPC174560
0.5672 Remote Similarity NPC273614
0.5672 Remote Similarity NPC113293
0.5667 Remote Similarity NPC27264
0.5667 Remote Similarity NPC221467
0.566 Remote Similarity NPC226511
0.566 Remote Similarity NPC180840
0.566 Remote Similarity NPC155880
0.566 Remote Similarity NPC34873
0.566 Remote Similarity NPC40434
0.566 Remote Similarity NPC92863
0.5652 Remote Similarity NPC255863
0.5652 Remote Similarity NPC317881
0.5652 Remote Similarity NPC476657
0.5652 Remote Similarity NPC478098
0.5652 Remote Similarity NPC320642
0.5652 Remote Similarity NPC326268
0.5652 Remote Similarity NPC476655
0.5652 Remote Similarity NPC476654
0.5652 Remote Similarity NPC478099
0.5652 Remote Similarity NPC323045
0.5652 Remote Similarity NPC318420
0.5652 Remote Similarity NPC245947
0.5652 Remote Similarity NPC136164
0.5647 Remote Similarity NPC319473
0.5645 Remote Similarity NPC477781
0.5645 Remote Similarity NPC217188
0.5645 Remote Similarity NPC71761
0.5645 Remote Similarity NPC477780
0.5625 Remote Similarity NPC82239
0.5625 Remote Similarity NPC324224
0.5625 Remote Similarity NPC472808
0.5616 Remote Similarity NPC66365
0.5606 Remote Similarity NPC222852

  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 NPC477779 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
0.7959 Intermediate Similarity NPD5326 Phase 3
0.7647 Intermediate Similarity NPD4222 Approved
0.7647 Intermediate Similarity NPD39 Approved
0.7222 Intermediate Similarity NPD3173 Approved
0.6792 Remote Similarity NPD6096 Approved
0.6792 Remote Similarity NPD6097 Approved
0.6724 Remote Similarity NPD3172 Approved
0.6667 Remote Similarity NPD3174 Discontinued
0.661 Remote Similarity NPD3195 Phase 2
0.661 Remote Similarity NPD4266 Approved
0.661 Remote Similarity NPD3196 Approved
0.661 Remote Similarity NPD3194 Approved
0.6429 Remote Similarity NPD5343 Approved
0.619 Remote Similarity NPD6109 Phase 1
0.6102 Remote Similarity NPD29 Approved
0.6102 Remote Similarity NPD28 Approved
0.6066 Remote Similarity NPD539 Approved
0.6034 Remote Similarity NPD4220 Pre-registration
0.6 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5862 Remote Similarity NPD622 Approved
0.5833 Remote Similarity NPD6927 Phase 3
0.5783 Remote Similarity NPD5370 Suspended
0.5735 Remote Similarity NPD3197 Phase 1
0.5714 Remote Similarity NPD9411 Phase 1
0.5647 Remote Similarity NPD4810 Clinical (unspecified phase)
0.561 Remote Similarity NPD6422 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