Structure

Physi-Chem Properties

Molecular Weight:  258.16
Volume:  301.713
LogP:  3.268
LogD:  3.507
LogS:  -3.842
# Rotatable Bonds:  8
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.399
Synthetic Accessibility Score:  4.073
Fsp3:  0.412
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.585
MDCK Permeability:  3.9592971006641164e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.065
20% Bioavailability (F20%):  0.996
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.013
Plasma Protein Binding (PPB):  100.79523468017578%
Volume Distribution (VD):  0.897
Pgp-substrate:  1.5485591888427734%

ADMET: Metabolism

CYP1A2-inhibitor:  0.789
CYP1A2-substrate:  0.19
CYP2C19-inhibitor:  0.947
CYP2C19-substrate:  0.641
CYP2C9-inhibitor:  0.917
CYP2C9-substrate:  0.985
CYP2D6-inhibitor:  0.698
CYP2D6-substrate:  0.865
CYP3A4-inhibitor:  0.923
CYP3A4-substrate:  0.246

ADMET: Excretion

Clearance (CL):  7.83
Half-life (T1/2):  0.883

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.564
Drug-inuced Liver Injury (DILI):  0.963
AMES Toxicity:  0.77
Rat Oral Acute Toxicity:  0.951
Maximum Recommended Daily Dose:  0.995
Skin Sensitization:  0.964
Carcinogencity:  0.503
Eye Corrosion:  0.964
Eye Irritation:  0.99
Respiratory Toxicity:  0.981

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

  Natural Product: NPC35141

Natural Product ID:  NPC35141
Common Name*:   Gymnasterkoreayne F
IUPAC Name:   (2E,8S,9Z)-heptadeca-2,9,16-trien-4,6-diyne-1,8-diol
Synonyms:   gymnasterkoreayne F
Standard InCHIKey:  UOQDNDFAPLNEJQ-RZTJKQGCSA-N
Standard InCHI:  InChI=1S/C17H22O2/c1-2-3-4-5-6-8-11-14-17(19)15-12-9-7-10-13-16-18/h2,10-11,13-14,17-19H,1,3-6,8,16H2/b13-10+,14-11-/t17-/m0/s1
SMILES:  C=CCCCCC/C=C[C@@H](C#CC#C/C=C/CO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL465856
PubChem CID:   10355169
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002951] Long-chain 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]
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]
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 = 3.1 ug ml-1 PMID[521581]

☑ 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 NPC35141 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
1.0 High Similarity NPC124183
0.9556 High Similarity NPC471280
0.9556 High Similarity NPC31194
0.9556 High Similarity NPC85079
0.9556 High Similarity NPC248884
0.9556 High Similarity NPC471275
0.9556 High Similarity NPC153538
0.9556 High Similarity NPC125122
0.9556 High Similarity NPC471276
0.9535 High Similarity NPC101616
0.9348 High Similarity NPC477727
0.9348 High Similarity NPC72699
0.9348 High Similarity NPC471281
0.9348 High Similarity NPC199286
0.9149 High Similarity NPC256656
0.9149 High Similarity NPC475477
0.9149 High Similarity NPC170776
0.9149 High Similarity NPC294278
0.9149 High Similarity NPC165447
0.9149 High Similarity NPC329608
0.9149 High Similarity NPC151782
0.9149 High Similarity NPC224148
0.9149 High Similarity NPC89824
0.9149 High Similarity NPC477723
0.9149 High Similarity NPC93639
0.9149 High Similarity NPC76198
0.9149 High Similarity NPC55383
0.9149 High Similarity NPC9273
0.9149 High Similarity NPC197272
0.9149 High Similarity NPC471959
0.9111 High Similarity NPC55063
0.9111 High Similarity NPC19834
0.8958 High Similarity NPC142092
0.8936 High Similarity NPC249670
0.8936 High Similarity NPC473913
0.8936 High Similarity NPC474642
0.8889 High Similarity NPC269074
0.875 High Similarity NPC71053
0.875 High Similarity NPC59408
0.8696 High Similarity NPC180575
0.8636 High Similarity NPC304151
0.86 High Similarity NPC49059
0.86 High Similarity NPC110732
0.86 High Similarity NPC48058
0.86 High Similarity NPC256209
0.86 High Similarity NPC473532
0.8542 High Similarity NPC328784
0.8542 High Similarity NPC291437
0.8431 Intermediate Similarity NPC477725
0.8431 Intermediate Similarity NPC473735
0.8431 Intermediate Similarity NPC477726
0.8431 Intermediate Similarity NPC470963
0.8431 Intermediate Similarity NPC474513
0.8431 Intermediate Similarity NPC146551
0.8431 Intermediate Similarity NPC152668
0.8431 Intermediate Similarity NPC473725
0.8431 Intermediate Similarity NPC471239
0.8431 Intermediate Similarity NPC475353
0.8431 Intermediate Similarity NPC473910
0.8431 Intermediate Similarity NPC473896
0.8431 Intermediate Similarity NPC473721
0.8367 Intermediate Similarity NPC129263
0.8333 Intermediate Similarity NPC302310
0.8298 Intermediate Similarity NPC157096
0.8269 Intermediate Similarity NPC473847
0.8269 Intermediate Similarity NPC470969
0.8269 Intermediate Similarity NPC470964
0.8269 Intermediate Similarity NPC475384
0.8269 Intermediate Similarity NPC470966
0.8269 Intermediate Similarity NPC471960
0.8269 Intermediate Similarity NPC161838
0.8269 Intermediate Similarity NPC470968
0.8269 Intermediate Similarity NPC470967
0.8269 Intermediate Similarity NPC477661
0.8269 Intermediate Similarity NPC311648
0.8222 Intermediate Similarity NPC149668
0.8182 Intermediate Similarity NPC103236
0.8182 Intermediate Similarity NPC329762
0.8182 Intermediate Similarity NPC27444
0.8113 Intermediate Similarity NPC212730
0.8113 Intermediate Similarity NPC594
0.8113 Intermediate Similarity NPC470970
0.8113 Intermediate Similarity NPC48968
0.8113 Intermediate Similarity NPC265551
0.8113 Intermediate Similarity NPC193975
0.8077 Intermediate Similarity NPC474644
0.8039 Intermediate Similarity NPC34577
0.8039 Intermediate Similarity NPC61177
0.7955 Intermediate Similarity NPC15934
0.7925 Intermediate Similarity NPC473865
0.7925 Intermediate Similarity NPC474643
0.7872 Intermediate Similarity NPC108195
0.7826 Intermediate Similarity NPC206906
0.7818 Intermediate Similarity NPC473652
0.78 Intermediate Similarity NPC473768
0.7778 Intermediate Similarity NPC44542
0.7708 Intermediate Similarity NPC276825
0.7692 Intermediate Similarity NPC187361
0.7692 Intermediate Similarity NPC26102
0.7692 Intermediate Similarity NPC477724
0.7679 Intermediate Similarity NPC471278
0.7674 Intermediate Similarity NPC213767
0.7647 Intermediate Similarity NPC473672
0.7647 Intermediate Similarity NPC474495
0.7544 Intermediate Similarity NPC66460
0.7544 Intermediate Similarity NPC168407
0.7544 Intermediate Similarity NPC271282
0.7544 Intermediate Similarity NPC325929
0.7544 Intermediate Similarity NPC475984
0.75 Intermediate Similarity NPC216416
0.7455 Intermediate Similarity NPC472445
0.7414 Intermediate Similarity NPC470965
0.7414 Intermediate Similarity NPC29697
0.7358 Intermediate Similarity NPC284224
0.7358 Intermediate Similarity NPC474496
0.7308 Intermediate Similarity NPC29234
0.7292 Intermediate Similarity NPC116934
0.7255 Intermediate Similarity NPC475153
0.7234 Intermediate Similarity NPC269823
0.7193 Intermediate Similarity NPC222852
0.7174 Intermediate Similarity NPC182840
0.7174 Intermediate Similarity NPC306850
0.7174 Intermediate Similarity NPC29091
0.7174 Intermediate Similarity NPC255042
0.7174 Intermediate Similarity NPC103213
0.717 Intermediate Similarity NPC35756
0.7143 Intermediate Similarity NPC138935
0.7115 Intermediate Similarity NPC475071
0.7115 Intermediate Similarity NPC474460
0.7091 Intermediate Similarity NPC317899
0.7083 Intermediate Similarity NPC31121
0.7083 Intermediate Similarity NPC256766
0.7083 Intermediate Similarity NPC213538
0.7083 Intermediate Similarity NPC46248
0.7083 Intermediate Similarity NPC249801
0.7045 Intermediate Similarity NPC58957
0.7037 Intermediate Similarity NPC217188
0.7018 Intermediate Similarity NPC181872
0.7 Intermediate Similarity NPC474202
0.7 Intermediate Similarity NPC226592
0.7 Intermediate Similarity NPC470320
0.7 Intermediate Similarity NPC160628
0.7 Intermediate Similarity NPC474362
0.7 Intermediate Similarity NPC140501
0.6949 Remote Similarity NPC477829
0.6935 Remote Similarity NPC473752
0.6923 Remote Similarity NPC267110
0.6852 Remote Similarity NPC473705
0.6842 Remote Similarity NPC471279
0.6842 Remote Similarity NPC121034
0.6842 Remote Similarity NPC471277
0.6818 Remote Similarity NPC250734
0.6792 Remote Similarity NPC182102
0.6792 Remote Similarity NPC26960
0.6792 Remote Similarity NPC473487
0.6792 Remote Similarity NPC20934
0.6792 Remote Similarity NPC288381
0.6786 Remote Similarity NPC329686
0.6786 Remote Similarity NPC227135
0.678 Remote Similarity NPC327112
0.6727 Remote Similarity NPC475723
0.6724 Remote Similarity NPC226848
0.6667 Remote Similarity NPC76976
0.6667 Remote Similarity NPC200772
0.6667 Remote Similarity NPC472808
0.6667 Remote Similarity NPC324224
0.661 Remote Similarity NPC473866
0.661 Remote Similarity NPC475931
0.661 Remote Similarity NPC474267
0.661 Remote Similarity NPC122239
0.6607 Remote Similarity NPC300121
0.6607 Remote Similarity NPC269615
0.6607 Remote Similarity NPC189677
0.66 Remote Similarity NPC252978
0.6596 Remote Similarity NPC40434
0.6596 Remote Similarity NPC34873
0.6557 Remote Similarity NPC55068
0.6552 Remote Similarity NPC474577
0.6545 Remote Similarity NPC106531
0.6522 Remote Similarity NPC79544
0.6491 Remote Similarity NPC474913
0.6491 Remote Similarity NPC251666
0.6491 Remote Similarity NPC232247
0.6471 Remote Similarity NPC474413
0.6471 Remote Similarity NPC473539
0.6471 Remote Similarity NPC267514
0.6471 Remote Similarity NPC145755
0.6444 Remote Similarity NPC62779
0.6444 Remote Similarity NPC81989
0.6441 Remote Similarity NPC469373
0.6441 Remote Similarity NPC155025
0.6415 Remote Similarity NPC471958
0.6393 Remote Similarity NPC26810
0.6393 Remote Similarity NPC113293
0.6383 Remote Similarity NPC174396
0.6379 Remote Similarity NPC48891
0.6379 Remote Similarity NPC249645
0.6379 Remote Similarity NPC55412
0.6364 Remote Similarity NPC244038
0.6364 Remote Similarity NPC196831

  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 NPC35141 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 NPD4265 Approved
0.678 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6557 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6379 Remote Similarity NPD4219 Approved
0.6167 Remote Similarity NPD585 Clinical (unspecified phase)
0.6129 Remote Similarity NPD368 Approved
0.6 Remote Similarity NPD4220 Pre-registration
0.5932 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5932 Remote Similarity NPD342 Phase 1
0.5909 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5882 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5741 Remote Similarity NPD39 Approved
0.5714 Remote Similarity NPD4732 Discontinued
0.5692 Remote Similarity NPD3197 Phase 1
0.5614 Remote Similarity NPD2268 Discontinued

  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