Structure

Physi-Chem Properties

Molecular Weight:  232.08
Volume:  227.277
LogP:  -1.231
LogD:  -0.54
LogS:  -2.331
# Rotatable Bonds:  8
TPSA:  63.6
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.396
Synthetic Accessibility Score:  3.163
Fsp3:  0.4
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:  -5.275
MDCK Permeability:  2.0472934920690022e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.053
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.006
Plasma Protein Binding (PPB):  94.05928802490234%
Volume Distribution (VD):  0.396
Pgp-substrate:  2.112011671066284%

ADMET: Metabolism

CYP1A2-inhibitor:  0.006
CYP1A2-substrate:  0.587
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.105
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.936
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.588
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.036

ADMET: Excretion

Clearance (CL):  3.877
Half-life (T1/2):  0.901

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.365
Drug-inuced Liver Injury (DILI):  0.006
AMES Toxicity:  0.986
Rat Oral Acute Toxicity:  0.021
Maximum Recommended Daily Dose:  0.581
Skin Sensitization:  0.96
Carcinogencity:  0.87
Eye Corrosion:  0.978
Eye Irritation:  0.957
Respiratory Toxicity:  0.981

Download Data

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

  Natural Product: NPC195109

Natural Product ID:  NPC195109
Common Name*:   (3Z,6Z)-3,6,9-Decatrienyl Sulfate
IUPAC Name:   [(3Z,6Z)-deca-3,6,9-trienyl] hydrogen sulfate
Synonyms:   (3Z,6Z)-3,6,9-Decatrienyl Sulfate
Standard InCHIKey:  QIMWCSPXMQZZSR-UTOQUPLUSA-N
Standard InCHI:  InChI=1S/C10H16O4S/c1-2-3-4-5-6-7-8-9-10-14-15(11,12)13/h2,4-5,7-8H,1,3,6,9-10H2,(H,11,12,13)/b5-4-,8-7-
SMILES:  C=CC/C=CC/C=CCCOS(=O)(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL460439
PubChem CID:   10399046
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000403] Organic sulfuric acids and derivatives
        • [CHEMONTID:0003455] Sulfuric acid esters
          • [CHEMONTID:0001185] Sulfuric acid monoesters

*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
NPO21633 Halocynthia roretzi Species Pyuridae Eukaryota n.a. n.a. n.a. PMID[7853012]
NPO21633 Halocynthia roretzi Species Pyuridae 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
NPT1845 Organism Vibrio alginolyticus Vibrio alginolyticus IZ = 12.0 mm PMID[506773]
NPT5959 Organism Umbelopsis ramanniana Umbelopsis ramanniana IZ = 10.0 mm PMID[506773]

☑ 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 NPC195109 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
0.8919 High Similarity NPC171978
0.8919 High Similarity NPC277382
0.8462 Intermediate Similarity NPC469713
0.6842 Remote Similarity NPC197356
0.6842 Remote Similarity NPC63121
0.6512 Remote Similarity NPC123357
0.6429 Remote Similarity NPC34873
0.6429 Remote Similarity NPC40434
0.6429 Remote Similarity NPC226511
0.6279 Remote Similarity NPC15934
0.625 Remote Similarity NPC250734
0.6222 Remote Similarity NPC187922
0.6136 Remote Similarity NPC103236
0.6136 Remote Similarity NPC27444
0.6136 Remote Similarity NPC329762
0.6098 Remote Similarity NPC58957
0.5909 Remote Similarity NPC182840
0.5909 Remote Similarity NPC255042
0.5909 Remote Similarity NPC57011
0.5909 Remote Similarity NPC103213
0.5909 Remote Similarity NPC29091
0.5893 Remote Similarity NPC329424
0.587 Remote Similarity NPC149668
0.587 Remote Similarity NPC206906
0.587 Remote Similarity NPC304151
0.5833 Remote Similarity NPC221379
0.5833 Remote Similarity NPC160628
0.58 Remote Similarity NPC477778
0.5778 Remote Similarity NPC56917
0.5745 Remote Similarity NPC252978
0.5745 Remote Similarity NPC116934
0.5714 Remote Similarity NPC72258
0.5714 Remote Similarity NPC35141
0.5714 Remote Similarity NPC157096
0.5714 Remote Similarity NPC124183
0.566 Remote Similarity NPC475723
0.5652 Remote Similarity NPC33489
0.5652 Remote Similarity NPC269823
0.5625 Remote Similarity NPC101616
0.5625 Remote Similarity NPC138935
0.5625 Remote Similarity NPC108195
0.56 Remote Similarity NPC318549

  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 NPC195109 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
0.5625 Remote Similarity NPD6096 Approved
0.5625 Remote Similarity NPD6097 Approved

  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