Structure

Physi-Chem Properties

Molecular Weight:  258.16
Volume:  295.793
LogP:  4.098
LogD:  3.941
LogS:  -4.333
# Rotatable Bonds:  7
TPSA:  32.76
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.33
Synthetic Accessibility Score:  4.547
Fsp3:  0.529
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.62
MDCK Permeability:  2.112249239871744e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.373
20% Bioavailability (F20%):  0.975
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.189
Plasma Protein Binding (PPB):  101.01763153076172%
Volume Distribution (VD):  1.819
Pgp-substrate:  1.5539592504501343%

ADMET: Metabolism

CYP1A2-inhibitor:  0.355
CYP1A2-substrate:  0.786
CYP2C19-inhibitor:  0.762
CYP2C19-substrate:  0.786
CYP2C9-inhibitor:  0.861
CYP2C9-substrate:  0.958
CYP2D6-inhibitor:  0.054
CYP2D6-substrate:  0.664
CYP3A4-inhibitor:  0.877
CYP3A4-substrate:  0.223

ADMET: Excretion

Clearance (CL):  8.62
Half-life (T1/2):  0.579

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.163
Drug-inuced Liver Injury (DILI):  0.942
AMES Toxicity:  0.68
Rat Oral Acute Toxicity:  0.979
Maximum Recommended Daily Dose:  0.995
Skin Sensitization:  0.944
Carcinogencity:  0.329
Eye Corrosion:  0.935
Eye Irritation:  0.975
Respiratory Toxicity:  0.979

Download Data

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

  Natural Product: NPC142092

Natural Product ID:  NPC142092
Common Name*:   Gymnasterkoreayne B
IUPAC Name:   (5S,6Z)-1-(3-methyloxiran-2-yl)tetradeca-6,13-dien-1,3-diyn-5-ol
Synonyms:   Gymnasterkoreayne B
Standard InCHIKey:  HEYJULODWUSFKN-VVNQDVNCSA-N
Standard InCHI:  InChI=1S/C17H22O2/c1-3-4-5-6-7-8-9-12-16(18)13-10-11-14-17-15(2)19-17/h3,9,12,15-18H,1,4-8H2,2H3/b12-9-/t15?,16-,17?/m0/s1
SMILES:  C=CCCCCC/C=C[C@@H](C#CC#CC1C(C)O1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL452639
PubChem CID:   10264498
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]
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]
NPO15816 Gymnaster koraiensis n.a. n.a. n.a. 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 = 3.3 ug ml-1 PMID[524026]
NPT440 Individual Protein Quinone oxidoreductase Mus musculus Drug uptake = 7.38 uM PMID[524027]
NPT27 Others Unspecified IC50 = 70590.0 nM PMID[524027]
NPT2 Others Unspecified Ratio IC50 = 9.57 n.a. PMID[524027]

☑ 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 NPC142092 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
0.898 High Similarity NPC153538
0.898 High Similarity NPC31194
0.898 High Similarity NPC248884
0.898 High Similarity NPC85079
0.8958 High Similarity NPC35141
0.8958 High Similarity NPC124183
0.88 High Similarity NPC72699
0.8627 High Similarity NPC93639
0.8627 High Similarity NPC151782
0.86 High Similarity NPC471280
0.86 High Similarity NPC125122
0.86 High Similarity NPC471275
0.86 High Similarity NPC471276
0.8571 High Similarity NPC55063
0.8571 High Similarity NPC19834
0.8542 High Similarity NPC101616
0.8431 Intermediate Similarity NPC199286
0.8431 Intermediate Similarity NPC474642
0.8431 Intermediate Similarity NPC249670
0.8431 Intermediate Similarity NPC473913
0.8431 Intermediate Similarity NPC477727
0.8431 Intermediate Similarity NPC471281
0.8367 Intermediate Similarity NPC269074
0.8364 Intermediate Similarity NPC265551
0.8364 Intermediate Similarity NPC212730
0.8269 Intermediate Similarity NPC170776
0.8269 Intermediate Similarity NPC165447
0.8269 Intermediate Similarity NPC256656
0.8269 Intermediate Similarity NPC71053
0.8269 Intermediate Similarity NPC294278
0.8269 Intermediate Similarity NPC89824
0.8269 Intermediate Similarity NPC329608
0.8269 Intermediate Similarity NPC59408
0.8269 Intermediate Similarity NPC475477
0.8269 Intermediate Similarity NPC477723
0.8269 Intermediate Similarity NPC197272
0.8269 Intermediate Similarity NPC76198
0.8269 Intermediate Similarity NPC55383
0.8269 Intermediate Similarity NPC224148
0.8269 Intermediate Similarity NPC9273
0.8269 Intermediate Similarity NPC471959
0.82 Intermediate Similarity NPC180575
0.8148 Intermediate Similarity NPC49059
0.8148 Intermediate Similarity NPC110732
0.8148 Intermediate Similarity NPC256209
0.8125 Intermediate Similarity NPC304151
0.8077 Intermediate Similarity NPC291437
0.8077 Intermediate Similarity NPC328784
0.8036 Intermediate Similarity NPC193975
0.8036 Intermediate Similarity NPC44542
0.7931 Intermediate Similarity NPC471278
0.7885 Intermediate Similarity NPC302310
0.7818 Intermediate Similarity NPC48058
0.7818 Intermediate Similarity NPC473532
0.7797 Intermediate Similarity NPC66460
0.7797 Intermediate Similarity NPC271282
0.7797 Intermediate Similarity NPC325929
0.7719 Intermediate Similarity NPC472445
0.7679 Intermediate Similarity NPC477726
0.7679 Intermediate Similarity NPC473721
0.7679 Intermediate Similarity NPC474644
0.7679 Intermediate Similarity NPC470963
0.7679 Intermediate Similarity NPC473725
0.7679 Intermediate Similarity NPC475353
0.7679 Intermediate Similarity NPC146551
0.7679 Intermediate Similarity NPC152668
0.7679 Intermediate Similarity NPC473896
0.7679 Intermediate Similarity NPC471239
0.7679 Intermediate Similarity NPC474513
0.7679 Intermediate Similarity NPC473910
0.7679 Intermediate Similarity NPC473735
0.7679 Intermediate Similarity NPC477725
0.7667 Intermediate Similarity NPC29697
0.7636 Intermediate Similarity NPC61177
0.7593 Intermediate Similarity NPC129263
0.7544 Intermediate Similarity NPC473847
0.7544 Intermediate Similarity NPC470966
0.7544 Intermediate Similarity NPC470968
0.7544 Intermediate Similarity NPC470964
0.7544 Intermediate Similarity NPC471960
0.7544 Intermediate Similarity NPC477661
0.7544 Intermediate Similarity NPC475384
0.7544 Intermediate Similarity NPC474643
0.7544 Intermediate Similarity NPC470969
0.7544 Intermediate Similarity NPC470967
0.7544 Intermediate Similarity NPC473865
0.7544 Intermediate Similarity NPC161838
0.7544 Intermediate Similarity NPC311648
0.75 Intermediate Similarity NPC157096
0.75 Intermediate Similarity NPC15934
0.7458 Intermediate Similarity NPC222852
0.7451 Intermediate Similarity NPC108195
0.7414 Intermediate Similarity NPC474577
0.7414 Intermediate Similarity NPC48968
0.7414 Intermediate Similarity NPC594
0.7414 Intermediate Similarity NPC470970
0.74 Intermediate Similarity NPC206906
0.74 Intermediate Similarity NPC149668
0.7347 Intermediate Similarity NPC27444
0.7347 Intermediate Similarity NPC329762
0.7347 Intermediate Similarity NPC103236
0.7321 Intermediate Similarity NPC34577
0.7308 Intermediate Similarity NPC276825
0.7273 Intermediate Similarity NPC473672
0.7273 Intermediate Similarity NPC474495
0.7273 Intermediate Similarity NPC29234
0.7167 Intermediate Similarity NPC473652
0.7119 Intermediate Similarity NPC471279
0.7119 Intermediate Similarity NPC471277
0.7091 Intermediate Similarity NPC473768
0.7059 Intermediate Similarity NPC31121
0.7018 Intermediate Similarity NPC477724
0.7018 Intermediate Similarity NPC284224
0.7018 Intermediate Similarity NPC26102
0.7018 Intermediate Similarity NPC187361
0.7018 Intermediate Similarity NPC474496
0.6984 Remote Similarity NPC475221
0.6935 Remote Similarity NPC168407
0.6935 Remote Similarity NPC475984
0.6923 Remote Similarity NPC473752
0.6923 Remote Similarity NPC116934
0.6897 Remote Similarity NPC269615
0.6885 Remote Similarity NPC474267
0.6875 Remote Similarity NPC213767
0.6863 Remote Similarity NPC269823
0.6842 Remote Similarity NPC35756
0.6842 Remote Similarity NPC106531
0.6833 Remote Similarity NPC121034
0.6825 Remote Similarity NPC470965
0.68 Remote Similarity NPC103213
0.68 Remote Similarity NPC29091
0.68 Remote Similarity NPC182840
0.68 Remote Similarity NPC255042
0.6792 Remote Similarity NPC138935
0.6786 Remote Similarity NPC475071
0.6786 Remote Similarity NPC474460
0.678 Remote Similarity NPC317899
0.678 Remote Similarity NPC474913
0.6774 Remote Similarity NPC258788
0.6735 Remote Similarity NPC216416
0.6731 Remote Similarity NPC249801
0.6731 Remote Similarity NPC46248
0.6731 Remote Similarity NPC256766
0.6731 Remote Similarity NPC213538
0.6724 Remote Similarity NPC217188
0.6721 Remote Similarity NPC469373
0.6721 Remote Similarity NPC181872
0.6719 Remote Similarity NPC226592
0.6719 Remote Similarity NPC470320
0.6667 Remote Similarity NPC259299
0.6667 Remote Similarity NPC140501
0.6667 Remote Similarity NPC327388
0.6667 Remote Similarity NPC26810
0.6667 Remote Similarity NPC58957
0.6667 Remote Similarity NPC474202
0.6667 Remote Similarity NPC160628
0.6667 Remote Similarity NPC474362
0.6667 Remote Similarity NPC113293
0.6613 Remote Similarity NPC473866
0.6607 Remote Similarity NPC267110
0.6607 Remote Similarity NPC475153
0.6567 Remote Similarity NPC305698
0.6557 Remote Similarity NPC211752
0.6557 Remote Similarity NPC323498
0.6557 Remote Similarity NPC323597
0.6552 Remote Similarity NPC473705
0.6508 Remote Similarity NPC327112
0.65 Remote Similarity NPC227135
0.65 Remote Similarity NPC329686
0.6491 Remote Similarity NPC473487
0.6491 Remote Similarity NPC182102
0.6491 Remote Similarity NPC26960
0.6491 Remote Similarity NPC20934
0.6491 Remote Similarity NPC288381
0.6471 Remote Similarity NPC239373
0.6471 Remote Similarity NPC329989
0.6471 Remote Similarity NPC304690
0.6471 Remote Similarity NPC74722
0.6471 Remote Similarity NPC306850
0.6458 Remote Similarity NPC250734
0.6452 Remote Similarity NPC226848
0.6406 Remote Similarity NPC477829
0.6406 Remote Similarity NPC55376
0.6406 Remote Similarity NPC328776
0.6406 Remote Similarity NPC320305
0.6393 Remote Similarity NPC472808
0.6393 Remote Similarity NPC324224
0.6364 Remote Similarity NPC76976
0.6349 Remote Similarity NPC83838
0.6349 Remote Similarity NPC122239
0.6349 Remote Similarity NPC478095
0.6349 Remote Similarity NPC143810
0.6349 Remote Similarity NPC475931
0.6333 Remote Similarity NPC300121
0.6333 Remote Similarity NPC189677
0.6308 Remote Similarity NPC55068
0.6296 Remote Similarity NPC252978
0.629 Remote Similarity NPC474869
0.629 Remote Similarity NPC129150
0.6275 Remote Similarity NPC34873

  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 NPC142092 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
0.7 Intermediate Similarity NPD585 Clinical (unspecified phase)
0.6667 Remote Similarity NPD4265 Approved
0.6508 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6308 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6129 Remote Similarity NPD4219 Approved
0.5909 Remote Similarity NPD368 Approved
0.5882 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5763 Remote Similarity NPD4220 Pre-registration
0.5714 Remote Similarity NPD342 Phase 1
0.5714 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5714 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5694 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5692 Remote Similarity NPD6109 Phase 1
0.5667 Remote Similarity NPD2268 Discontinued
0.5614 Remote Similarity NPD6096 Approved
0.5614 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