Structure

Physi-Chem Properties

Molecular Weight:  164.08
Volume:  185.914
LogP:  1.061
LogD:  0.339
LogS:  -1.307
# Rotatable Bonds:  2
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.577
Synthetic Accessibility Score:  4.373
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.067
MDCK Permeability:  0.00043514042044989765
Pgp-inhibitor:  0.002
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.21
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.085
Plasma Protein Binding (PPB):  97.34209442138672%
Volume Distribution (VD):  0.994
Pgp-substrate:  2.845341920852661%

ADMET: Metabolism

CYP1A2-inhibitor:  0.485
CYP1A2-substrate:  0.207
CYP2C19-inhibitor:  0.933
CYP2C19-substrate:  0.777
CYP2C9-inhibitor:  0.887
CYP2C9-substrate:  0.971
CYP2D6-inhibitor:  0.336
CYP2D6-substrate:  0.611
CYP3A4-inhibitor:  0.54
CYP3A4-substrate:  0.214

ADMET: Excretion

Clearance (CL):  7.424
Half-life (T1/2):  0.742

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.904
Drug-inuced Liver Injury (DILI):  0.982
AMES Toxicity:  0.973
Rat Oral Acute Toxicity:  0.987
Maximum Recommended Daily Dose:  0.991
Skin Sensitization:  0.937
Carcinogencity:  0.441
Eye Corrosion:  0.962
Eye Irritation:  0.993
Respiratory Toxicity:  0.976

Download Data

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

  Natural Product: NPC174396

Natural Product ID:  NPC174396
Common Name*:   Gymnasterkoreayne A
IUPAC Name:   (E,3R)-dec-8-en-4,6-diyne-1,3-diol
Synonyms:  
Standard InCHIKey:  ZIRUVVYZSHKYCQ-PBKGFPTLSA-N
Standard InCHI:  InChI=1S/C10H12O2/c1-2-3-4-5-6-7-10(12)8-9-11/h2-3,10-12H,8-9H2,1H3/b3-2+/t10-/m0/s1
SMILES:  C/C=C/C#CC#C[C@@H](CCO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL463634
PubChem CID:   636738
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols

*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
NPO15816 Gymnaster koraiensis n.a. n.a. n.a. n.a. n.a. n.a. PMID[12088435]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. fruit n.a. PMID[17262892]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. fruit n.a. PMID[21163339]
NPO23708 Aster koraiensis Species Asteraceae Eukaryota aerial parts Euidang-myun, Gongju city, Chungchengnam-do, Republic of Korea 2007-Aug PMID[22264115]
NPO15816 Gymnaster koraiensis n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO15816 Gymnaster koraiensis n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO14730 Bonnetia dinizii Species Bonnetiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2090 Baccharis thesioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO368 Dendroaspis angusticeps Species Elapidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18458 Raukaua simplex Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23708 Aster koraiensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15816 Gymnaster koraiensis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO5406 Veronica chamaedrys Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9385 Glycosmis ovoidea Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14084 Roccella fucoides Species Roccellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2509 Strombus gigas Species Strombidae 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
NPT137 Cell Line L1210 Mus musculus ED50 > 10.0 ug ml-1 PMID[448999]
NPT35 Others n.a. IC50 > 50000.0 nM PMID[449000]
NPT68 Individual Protein Aldose reductase Rattus norvegicus IC50 > 30000.0 nM PMID[449000]

☑ 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 NPC174396 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
0.8421 Intermediate Similarity NPC306850
0.7174 Intermediate Similarity NPC302310
0.7021 Intermediate Similarity NPC328784
0.7021 Intermediate Similarity NPC291437
0.6889 Remote Similarity NPC201948
0.6875 Remote Similarity NPC151782
0.6809 Remote Similarity NPC153538
0.6765 Remote Similarity NPC88887
0.675 Remote Similarity NPC79544
0.6744 Remote Similarity NPC473625
0.6739 Remote Similarity NPC157096
0.6667 Remote Similarity NPC81989
0.6667 Remote Similarity NPC473487
0.6667 Remote Similarity NPC108195
0.6667 Remote Similarity NPC72699
0.6531 Remote Similarity NPC29234
0.6531 Remote Similarity NPC71053
0.6531 Remote Similarity NPC59408
0.6531 Remote Similarity NPC93639
0.6522 Remote Similarity NPC276825
0.6471 Remote Similarity NPC49059
0.6471 Remote Similarity NPC110732
0.6471 Remote Similarity NPC256209
0.6458 Remote Similarity NPC31194
0.6458 Remote Similarity NPC85079
0.6458 Remote Similarity NPC248884
0.6429 Remote Similarity NPC34873
0.6429 Remote Similarity NPC40434
0.641 Remote Similarity NPC197356
0.641 Remote Similarity NPC63121
0.64 Remote Similarity NPC473705
0.6383 Remote Similarity NPC19834
0.6383 Remote Similarity NPC55063
0.6383 Remote Similarity NPC35141
0.6383 Remote Similarity NPC124183
0.6341 Remote Similarity NPC213767
0.6327 Remote Similarity NPC473768
0.6304 Remote Similarity NPC101616
0.6304 Remote Similarity NPC474413
0.6304 Remote Similarity NPC473539
0.6275 Remote Similarity NPC284224
0.6275 Remote Similarity NPC477724
0.6275 Remote Similarity NPC187361
0.6275 Remote Similarity NPC26102
0.6222 Remote Similarity NPC249801
0.6222 Remote Similarity NPC46248
0.6222 Remote Similarity NPC304151
0.619 Remote Similarity NPC216416
0.6154 Remote Similarity NPC300121
0.6154 Remote Similarity NPC473532
0.6136 Remote Similarity NPC103236
0.6136 Remote Similarity NPC27444
0.6136 Remote Similarity NPC329762
0.6122 Remote Similarity NPC471275
0.6122 Remote Similarity NPC475153
0.6122 Remote Similarity NPC471280
0.6122 Remote Similarity NPC471276
0.6122 Remote Similarity NPC125122
0.6111 Remote Similarity NPC472445
0.6111 Remote Similarity NPC474577
0.6078 Remote Similarity NPC142092
0.6078 Remote Similarity NPC295765
0.6038 Remote Similarity NPC473725
0.6038 Remote Similarity NPC473896
0.6038 Remote Similarity NPC477725
0.6038 Remote Similarity NPC473721
0.6038 Remote Similarity NPC477726
0.6038 Remote Similarity NPC473735
0.6038 Remote Similarity NPC475353
0.6038 Remote Similarity NPC473910
0.6 Remote Similarity NPC473913
0.6 Remote Similarity NPC249670
0.6 Remote Similarity NPC474642
0.6 Remote Similarity NPC199286
0.6 Remote Similarity NPC477727
0.6 Remote Similarity NPC471281
0.6 Remote Similarity NPC245688
0.5962 Remote Similarity NPC475560
0.5946 Remote Similarity NPC320326
0.5926 Remote Similarity NPC471960
0.5926 Remote Similarity NPC475384
0.5926 Remote Similarity NPC161838
0.5926 Remote Similarity NPC470969
0.5926 Remote Similarity NPC470966
0.5926 Remote Similarity NPC477661
0.5926 Remote Similarity NPC470968
0.5926 Remote Similarity NPC470967
0.5926 Remote Similarity NPC473847
0.5897 Remote Similarity NPC28077
0.5897 Remote Similarity NPC242117
0.5882 Remote Similarity NPC89824
0.5882 Remote Similarity NPC294278
0.5882 Remote Similarity NPC470411
0.5882 Remote Similarity NPC329608
0.5882 Remote Similarity NPC471959
0.5882 Remote Similarity NPC299484
0.5882 Remote Similarity NPC9273
0.5882 Remote Similarity NPC129263
0.5882 Remote Similarity NPC224148
0.5882 Remote Similarity NPC55383
0.5882 Remote Similarity NPC477723
0.5882 Remote Similarity NPC76198
0.5882 Remote Similarity NPC256656
0.5882 Remote Similarity NPC170776
0.5882 Remote Similarity NPC165447
0.5882 Remote Similarity NPC197272
0.5882 Remote Similarity NPC475477
0.587 Remote Similarity NPC149668
0.587 Remote Similarity NPC206906
0.587 Remote Similarity NPC31121
0.5862 Remote Similarity NPC277570
0.5854 Remote Similarity NPC250734
0.5833 Remote Similarity NPC269074
0.5833 Remote Similarity NPC140389
0.5833 Remote Similarity NPC232554
0.5818 Remote Similarity NPC470970
0.5818 Remote Similarity NPC121034
0.5818 Remote Similarity NPC193975
0.5789 Remote Similarity NPC33415
0.5789 Remote Similarity NPC301586
0.5769 Remote Similarity NPC35756
0.5745 Remote Similarity NPC252978
0.5714 Remote Similarity NPC42304
0.5714 Remote Similarity NPC58957
0.5714 Remote Similarity NPC39977
0.5714 Remote Similarity NPC180575
0.5686 Remote Similarity NPC225974
0.5686 Remote Similarity NPC20934
0.5686 Remote Similarity NPC474460
0.5686 Remote Similarity NPC288381
0.5676 Remote Similarity NPC560
0.566 Remote Similarity NPC34577
0.566 Remote Similarity NPC474496
0.5652 Remote Similarity NPC474361
0.5625 Remote Similarity NPC62014
0.5614 Remote Similarity NPC222852
0.5614 Remote Similarity NPC473866

  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 NPC174396 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
0.5789 Remote Similarity NPD8549 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