Structure

Physi-Chem Properties

Molecular Weight:  305.13
Volume:  298.952
LogP:  -0.59
LogD:  -1.167
LogS:  -0.811
# Rotatable Bonds:  11
TPSA:  100.54
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.362
Synthetic Accessibility Score:  2.666
Fsp3:  0.692
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:  -5.507
MDCK Permeability:  1.0582356480881572e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.948
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.829
Plasma Protein Binding (PPB):  47.26683807373047%
Volume Distribution (VD):  0.437
Pgp-substrate:  57.96896743774414%

ADMET: Metabolism

CYP1A2-inhibitor:  0.005
CYP1A2-substrate:  0.097
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.083
CYP2C9-inhibitor:  0.025
CYP2C9-substrate:  0.895
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.097
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.061

ADMET: Excretion

Clearance (CL):  5.39
Half-life (T1/2):  0.808

ADMET: Toxicity

hERG Blockers:  0.032
Human Hepatotoxicity (H-HT):  0.067
Drug-inuced Liver Injury (DILI):  0.024
AMES Toxicity:  0.012
Rat Oral Acute Toxicity:  0.043
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.885
Carcinogencity:  0.016
Eye Corrosion:  0.135
Eye Irritation:  0.364
Respiratory Toxicity:  0.329

Download Data

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

  Natural Product: NPC476923

Natural Product ID:  NPC476923
Common Name*:   Deacyl irciniasulfonic acid C
IUPAC Name:   2-[[(Z)-3-methyl-9-oxodec-2-enoyl]amino]ethanesulfonic acid
Synonyms:  
Standard InCHIKey:  HNRYAWCNPZFIFM-KHPPLWFESA-N
Standard InCHI:  InChI=1S/C13H23NO5S/c1-11(6-4-3-5-7-12(2)15)10-13(16)14-8-9-20(17,18)19/h10H,3-9H2,1-2H3,(H,14,16)(H,17,18,19)/b11-10-
SMILES:  C/C(=C/C(=O)NCCS(=O)(=O)O)/CCCCCC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   90683099
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000331] Fatty amides
          • [CHEMONTID:0001096] N-acyl amines

*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
NPO33616 Coscinoderma sp. Species Spongiidae Eukaryota n.a. at a depth of 15 m off the coast of Weno Island, Chuuk state, Micronesia 2010-FEB PMID[24828374]
NPO33616 Coscinoderma sp. Species Spongiidae Eukaryota n.a. at a depth of 15 m off the coast of Weno Island, Chuuk state, Federated States of Micronesia 2010-FEB PMID[24828374]

☑ 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
NPT111 Cell Line K562 Homo sapiens LC50 > 100 ug/ml PMID[24828374]
NPT81 Cell Line A549 Homo sapiens LC50 > 100 ug/ml PMID[24828374]
NPT2 Others Unspecified IC50 > 100000 nM PMID[24828374]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 100 ug/ml PMID[24828374]
NPT3145 Organism Bacillus subtilis subsp. spizizenii ATCC 6633 Bacillus subtilis subsp. spizizenii ATCC 6633 MIC > 100 ug/ml PMID[24828374]
NPT3147 Organism Kocuria rhizophila Kocuria rhizophila MIC > 100 ug/ml PMID[24828374]
NPT1190 Organism Salmonella enterica Salmonella enterica MIC > 100 ug/ml PMID[24828374]
NPT2 Others Unspecified MIC > 100 ug/ml PMID[24828374]
NPT19 Organism Escherichia coli Escherichia coli MIC > 100 ug/ml PMID[24828374]

☑ 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 NPC476923 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
0.7692 Intermediate Similarity NPC476924
0.7568 Intermediate Similarity NPC187315
0.7027 Intermediate Similarity NPC324077
0.6892 Remote Similarity NPC6795
0.6364 Remote Similarity NPC273614
0.6316 Remote Similarity NPC312826
0.6216 Remote Similarity NPC273023
0.6133 Remote Similarity NPC104138
0.6133 Remote Similarity NPC261158
0.6133 Remote Similarity NPC306420
0.6133 Remote Similarity NPC24216
0.6053 Remote Similarity NPC245650
0.6027 Remote Similarity NPC195986
0.6026 Remote Similarity NPC309877
0.6026 Remote Similarity NPC130807
0.6 Remote Similarity NPC297020
0.5949 Remote Similarity NPC29468
0.5946 Remote Similarity NPC303672
0.5904 Remote Similarity NPC249713
0.5875 Remote Similarity NPC182758
0.5875 Remote Similarity NPC77891
0.5867 Remote Similarity NPC124382
0.5867 Remote Similarity NPC184014
0.5867 Remote Similarity NPC44193
0.5867 Remote Similarity NPC14234
0.5867 Remote Similarity NPC246519
0.5867 Remote Similarity NPC269800
0.5867 Remote Similarity NPC13011
0.5867 Remote Similarity NPC132669
0.5833 Remote Similarity NPC280065
0.5833 Remote Similarity NPC45060
0.5833 Remote Similarity NPC471022
0.5789 Remote Similarity NPC472614
0.5753 Remote Similarity NPC307435
0.5753 Remote Similarity NPC267692
0.5732 Remote Similarity NPC477525
0.5698 Remote Similarity NPC469836
0.5696 Remote Similarity NPC74617
0.5696 Remote Similarity NPC150505
0.5679 Remote Similarity NPC471023
0.5676 Remote Similarity NPC243539
0.5676 Remote Similarity NPC145032
0.5676 Remote Similarity NPC267340
0.5676 Remote Similarity NPC54542
0.5676 Remote Similarity NPC304223
0.5648 Remote Similarity NPC329305
0.561 Remote Similarity NPC150162

  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 NPC476923 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
NPD

  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