Structure

Physi-Chem Properties

Molecular Weight:  306.14
Volume:  300.27
LogP:  -1.103
LogD:  -1.688
LogS:  0.013
# Rotatable Bonds:  10
TPSA:  110.02
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.27
Synthetic Accessibility Score:  3.792
Fsp3:  0.769
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:  -5.692
MDCK Permeability:  0.00010386847861809656
Pgp-inhibitor:  0.0
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.93
20% Bioavailability (F20%):  0.981
30% Bioavailability (F30%):  0.834

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.957
Plasma Protein Binding (PPB):  43.90364074707031%
Volume Distribution (VD):  0.632
Pgp-substrate:  47.54801559448242%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.087
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.333
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.133
CYP2D6-inhibitor:  0.041
CYP2D6-substrate:  0.107
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.06

ADMET: Excretion

Clearance (CL):  3.708
Half-life (T1/2):  0.616

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.997
Drug-inuced Liver Injury (DILI):  0.013
AMES Toxicity:  0.513
Rat Oral Acute Toxicity:  0.051
Maximum Recommended Daily Dose:  0.328
Skin Sensitization:  0.924
Carcinogencity:  0.833
Eye Corrosion:  0.301
Eye Irritation:  0.508
Respiratory Toxicity:  0.973

Download Data

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

  Natural Product: NPC476924

Natural Product ID:  NPC476924
Common Name*:   sodium;2-[[(Z,9S)-9-hydroxy-3-methyldec-2-enoyl]amino]ethanesulfonate
IUPAC Name:   sodium;2-[[(Z,9S)-9-hydroxy-3-methyldec-2-enoyl]amino]ethanesulfonate
Synonyms:  
Standard InCHIKey:  VVSWTDKPFWMVFS-POTAGUDUSA-M
Standard InCHI:  InChI=1S/C13H25NO5S.Na/c1-11(6-4-3-5-7-12(2)15)10-13(16)14-8-9-20(17,18)19;/h10,12,15H,3-9H2,1-2H3,(H,14,16)(H,17,18,19);/q;+1/p-1/b11-10-;/t12-;/m0./s1
SMILES:  C[C@@H](CCCCC/C(=C\C(=O)NCCS(=O)(=O)[O-])/C)O.[Na+]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   90683100
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]
NPT1190 Organism Salmonella enterica Salmonella enterica MIC > 100 ug/ml PMID[24828374]
NPT2 Others Unspecified 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 NPC476924 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 NPC476923
0.6835 Remote Similarity NPC103712
0.6835 Remote Similarity NPC291196
0.68 Remote Similarity NPC324077
0.6757 Remote Similarity NPC326524
0.6757 Remote Similarity NPC329003
0.6757 Remote Similarity NPC325550
0.6711 Remote Similarity NPC471023
0.6707 Remote Similarity NPC288086
0.6667 Remote Similarity NPC130807
0.6622 Remote Similarity NPC321030
0.6585 Remote Similarity NPC314678
0.6579 Remote Similarity NPC29468
0.6329 Remote Similarity NPC477525
0.625 Remote Similarity NPC315141
0.625 Remote Similarity NPC129995
0.6235 Remote Similarity NPC264417
0.6235 Remote Similarity NPC217095
0.622 Remote Similarity NPC471022
0.6216 Remote Similarity NPC242930
0.6203 Remote Similarity NPC235311
0.6203 Remote Similarity NPC253468
0.618 Remote Similarity NPC82799
0.6164 Remote Similarity NPC474496
0.6111 Remote Similarity NPC473672
0.6111 Remote Similarity NPC474495
0.6104 Remote Similarity NPC74617
0.6104 Remote Similarity NPC312826
0.6104 Remote Similarity NPC150505
0.6 Remote Similarity NPC273023
0.6 Remote Similarity NPC469320
0.5943 Remote Similarity NPC329305
0.5921 Remote Similarity NPC306420
0.5921 Remote Similarity NPC261158
0.5921 Remote Similarity NPC104138
0.5921 Remote Similarity NPC24216
0.5904 Remote Similarity NPC249713
0.5897 Remote Similarity NPC122239
0.5895 Remote Similarity NPC34754
0.5895 Remote Similarity NPC324405
0.5882 Remote Similarity NPC474873
0.5876 Remote Similarity NPC319473
0.5875 Remote Similarity NPC316674
0.5867 Remote Similarity NPC256209
0.5867 Remote Similarity NPC49059
0.5862 Remote Similarity NPC51055
0.5862 Remote Similarity NPC140327
0.5862 Remote Similarity NPC62293
0.5862 Remote Similarity NPC212008
0.5843 Remote Similarity NPC469324
0.5833 Remote Similarity NPC45060
0.5833 Remote Similarity NPC280065
0.5823 Remote Similarity NPC309877
0.5811 Remote Similarity NPC195986
0.5806 Remote Similarity NPC477199
0.58 Remote Similarity NPC175614
0.5789 Remote Similarity NPC297020
0.5769 Remote Similarity NPC226848
0.5761 Remote Similarity NPC469833
0.5761 Remote Similarity NPC469838
0.5761 Remote Similarity NPC474312
0.5758 Remote Similarity NPC256570
0.5758 Remote Similarity NPC17290
0.5758 Remote Similarity NPC3568
0.5758 Remote Similarity NPC192066
0.575 Remote Similarity NPC273614
0.575 Remote Similarity NPC47333
0.5733 Remote Similarity NPC303672
0.5729 Remote Similarity NPC316186
0.5714 Remote Similarity NPC207657
0.5699 Remote Similarity NPC228638
0.5698 Remote Similarity NPC469836
0.5679 Remote Similarity NPC55068
0.5679 Remote Similarity NPC473508
0.5679 Remote Similarity NPC477106
0.5667 Remote Similarity NPC474833
0.5663 Remote Similarity NPC113224
0.5663 Remote Similarity NPC187315
0.5658 Remote Similarity NPC269800
0.5658 Remote Similarity NPC184014
0.5658 Remote Similarity NPC13011
0.5658 Remote Similarity NPC132669
0.5658 Remote Similarity NPC246519
0.5658 Remote Similarity NPC44193
0.5658 Remote Similarity NPC14234
0.5658 Remote Similarity NPC124382
0.5644 Remote Similarity NPC8098
0.5644 Remote Similarity NPC197294
0.5644 Remote Similarity NPC475503
0.5644 Remote Similarity NPC183449
0.5641 Remote Similarity NPC470970
0.5641 Remote Similarity NPC52012
0.5625 Remote Similarity NPC6795
0.5625 Remote Similarity NPC320478
0.5625 Remote Similarity NPC240506
0.5625 Remote Similarity NPC99487
0.5612 Remote Similarity NPC242503
0.5612 Remote Similarity NPC74672
0.5612 Remote Similarity NPC139782
0.5612 Remote Similarity NPC43074
0.5612 Remote Similarity NPC209047
0.561 Remote Similarity NPC300593
0.5604 Remote Similarity NPC477485
0.56 Remote Similarity NPC35269
0.56 Remote Similarity NPC262312
0.56 Remote Similarity NPC49494
0.56 Remote Similarity NPC70323
0.56 Remote Similarity NPC188341
0.56 Remote Similarity NPC23454

  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 NPC476924 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
0.58 Remote Similarity NPD4228 Discovery
0.5679 Remote Similarity NPD3210 Clinical (unspecified phase)
0.5648 Remote Similarity NPD6413 Approved
0.5612 Remote Similarity NPD8522 Clinical (unspecified phase)

  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