Structure

Physi-Chem Properties

Molecular Weight:  246.2
Volume:  298.196
LogP:  4.656
LogD:  3.635
LogS:  -4.138
# Rotatable Bonds:  9
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.369
Synthetic Accessibility Score:  3.036
Fsp3:  0.647
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:  -4.295
MDCK Permeability:  3.896048292517662e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.024
20% Bioavailability (F20%):  0.97
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  99.84557342529297%
Volume Distribution (VD):  2.236
Pgp-substrate:  0.9811172485351562%

ADMET: Metabolism

CYP1A2-inhibitor:  0.898
CYP1A2-substrate:  0.407
CYP2C19-inhibitor:  0.911
CYP2C19-substrate:  0.216
CYP2C9-inhibitor:  0.789
CYP2C9-substrate:  0.984
CYP2D6-inhibitor:  0.127
CYP2D6-substrate:  0.642
CYP3A4-inhibitor:  0.72
CYP3A4-substrate:  0.091

ADMET: Excretion

Clearance (CL):  8.094
Half-life (T1/2):  0.806

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.191
Drug-inuced Liver Injury (DILI):  0.888
AMES Toxicity:  0.16
Rat Oral Acute Toxicity:  0.032
Maximum Recommended Daily Dose:  0.035
Skin Sensitization:  0.965
Carcinogencity:  0.629
Eye Corrosion:  0.952
Eye Irritation:  0.988
Respiratory Toxicity:  0.893

Download Data

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

  Natural Product: NPC108195

Natural Product ID:  NPC108195
Common Name*:   Heptadec-9-Ene-4,6-Diyn-1-Ol
IUPAC Name:   (Z)-heptadec-9-en-4,6-diyn-1-ol
Synonyms:  
Standard InCHIKey:  TXNKJZICGHLGKD-HJWRWDBZSA-N
Standard InCHI:  InChI=1S/C17H26O/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18/h8-9,18H,2-7,10,15-17H2,1H3/b9-8-
SMILES:  CCCCCCC/C=CCC#CC#CCCCO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL337824
PubChem CID:   44360001
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
NPO18101 Cicuta virosa Species Apiaceae Eukaryota subterranean part n.a. n.a. PMID[11087575]
NPO18101 Cicuta virosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18101 Cicuta virosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18101 Cicuta virosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18101 Cicuta virosa Species Apiaceae 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
NPT32 Organism Mus musculus Mus musculus LD50 > 24.6 mg kg-1 i.p. PMID[469030]
NPT805 Protein Complex GABA-A receptor; anion channel Rattus norvegicus IC50 > 10000.0 nM PMID[469030]

☑ 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 NPC108195 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
0.9302 High Similarity NPC276825
0.9048 High Similarity NPC149668
0.8864 High Similarity NPC269074
0.8723 High Similarity NPC151782
0.8696 High Similarity NPC302310
0.8667 High Similarity NPC55063
0.8667 High Similarity NPC19834
0.8571 High Similarity NPC27444
0.8571 High Similarity NPC103236
0.8571 High Similarity NPC329762
0.8511 High Similarity NPC72699
0.8444 Intermediate Similarity NPC76976
0.8409 Intermediate Similarity NPC252978
0.8333 Intermediate Similarity NPC129263
0.8298 Intermediate Similarity NPC153538
0.8298 Intermediate Similarity NPC248884
0.8298 Intermediate Similarity NPC85079
0.8298 Intermediate Similarity NPC31194
0.8293 Intermediate Similarity NPC216416
0.8261 Intermediate Similarity NPC180575
0.8222 Intermediate Similarity NPC101616
0.82 Intermediate Similarity NPC49059
0.82 Intermediate Similarity NPC256209
0.8182 Intermediate Similarity NPC304151
0.8125 Intermediate Similarity NPC473913
0.8125 Intermediate Similarity NPC474642
0.8125 Intermediate Similarity NPC249670
0.8095 Intermediate Similarity NPC34873
0.8095 Intermediate Similarity NPC40434
0.8049 Intermediate Similarity NPC213767
0.8 Intermediate Similarity NPC187361
0.8 Intermediate Similarity NPC477724
0.8 Intermediate Similarity NPC284224
0.8 Intermediate Similarity NPC26102
0.8 Intermediate Similarity NPC34577
0.7959 Intermediate Similarity NPC59408
0.7959 Intermediate Similarity NPC71053
0.7959 Intermediate Similarity NPC93639
0.7917 Intermediate Similarity NPC125122
0.7917 Intermediate Similarity NPC471280
0.7917 Intermediate Similarity NPC471275
0.7917 Intermediate Similarity NPC471276
0.7872 Intermediate Similarity NPC35141
0.7872 Intermediate Similarity NPC157096
0.7872 Intermediate Similarity NPC124183
0.7843 Intermediate Similarity NPC473532
0.7843 Intermediate Similarity NPC110732
0.7755 Intermediate Similarity NPC199286
0.7755 Intermediate Similarity NPC328784
0.7755 Intermediate Similarity NPC471281
0.7755 Intermediate Similarity NPC291437
0.7755 Intermediate Similarity NPC477727
0.7692 Intermediate Similarity NPC473910
0.7692 Intermediate Similarity NPC473896
0.7692 Intermediate Similarity NPC473721
0.7692 Intermediate Similarity NPC473735
0.7692 Intermediate Similarity NPC477726
0.7692 Intermediate Similarity NPC475353
0.7692 Intermediate Similarity NPC473725
0.7692 Intermediate Similarity NPC477725
0.76 Intermediate Similarity NPC197272
0.76 Intermediate Similarity NPC89824
0.76 Intermediate Similarity NPC165447
0.76 Intermediate Similarity NPC9273
0.76 Intermediate Similarity NPC477723
0.76 Intermediate Similarity NPC170776
0.76 Intermediate Similarity NPC329608
0.76 Intermediate Similarity NPC294278
0.76 Intermediate Similarity NPC475477
0.76 Intermediate Similarity NPC224148
0.76 Intermediate Similarity NPC76198
0.76 Intermediate Similarity NPC55383
0.76 Intermediate Similarity NPC256656
0.76 Intermediate Similarity NPC471959
0.7547 Intermediate Similarity NPC470966
0.7547 Intermediate Similarity NPC473847
0.7547 Intermediate Similarity NPC470968
0.7547 Intermediate Similarity NPC470967
0.7547 Intermediate Similarity NPC471960
0.7547 Intermediate Similarity NPC475384
0.7547 Intermediate Similarity NPC470969
0.7547 Intermediate Similarity NPC477661
0.7547 Intermediate Similarity NPC161838
0.75 Intermediate Similarity NPC15934
0.7451 Intermediate Similarity NPC142092
0.7451 Intermediate Similarity NPC473705
0.7407 Intermediate Similarity NPC193975
0.7407 Intermediate Similarity NPC470970
0.74 Intermediate Similarity NPC473768
0.7391 Intermediate Similarity NPC206906
0.7358 Intermediate Similarity NPC474644
0.7273 Intermediate Similarity NPC469373
0.7255 Intermediate Similarity NPC474495
0.7255 Intermediate Similarity NPC29234
0.7255 Intermediate Similarity NPC473672
0.7222 Intermediate Similarity NPC474643
0.7222 Intermediate Similarity NPC473865
0.72 Intermediate Similarity NPC475153
0.717 Intermediate Similarity NPC48058
0.717 Intermediate Similarity NPC300121
0.7143 Intermediate Similarity NPC62779
0.7083 Intermediate Similarity NPC267514
0.7083 Intermediate Similarity NPC145755
0.7069 Intermediate Similarity NPC29697
0.7059 Intermediate Similarity NPC473487
0.7059 Intermediate Similarity NPC288381
0.7059 Intermediate Similarity NPC20934
0.7037 Intermediate Similarity NPC470963
0.7037 Intermediate Similarity NPC471239
0.7037 Intermediate Similarity NPC146551
0.7037 Intermediate Similarity NPC474513
0.7021 Intermediate Similarity NPC31121
0.7021 Intermediate Similarity NPC46248
0.7021 Intermediate Similarity NPC249801
0.6981 Remote Similarity NPC61177
0.6977 Remote Similarity NPC182392
0.6939 Remote Similarity NPC474202
0.6939 Remote Similarity NPC165651
0.6939 Remote Similarity NPC24824
0.6939 Remote Similarity NPC474362
0.6939 Remote Similarity NPC210560
0.6939 Remote Similarity NPC140501
0.6909 Remote Similarity NPC311648
0.6909 Remote Similarity NPC179764
0.6909 Remote Similarity NPC470964
0.6909 Remote Similarity NPC187777
0.6905 Remote Similarity NPC63121
0.6905 Remote Similarity NPC197356
0.6897 Remote Similarity NPC66460
0.6897 Remote Similarity NPC475984
0.6897 Remote Similarity NPC271282
0.6897 Remote Similarity NPC325929
0.6875 Remote Similarity NPC116934
0.6842 Remote Similarity NPC473866
0.6842 Remote Similarity NPC222852
0.6809 Remote Similarity NPC269823
0.6786 Remote Similarity NPC212730
0.6786 Remote Similarity NPC44542
0.6786 Remote Similarity NPC121034
0.6786 Remote Similarity NPC265551
0.6786 Remote Similarity NPC594
0.6786 Remote Similarity NPC472445
0.6786 Remote Similarity NPC48968
0.678 Remote Similarity NPC470965
0.6739 Remote Similarity NPC103213
0.6739 Remote Similarity NPC255042
0.6739 Remote Similarity NPC182840
0.6739 Remote Similarity NPC29091
0.6735 Remote Similarity NPC138935
0.6731 Remote Similarity NPC26960
0.6731 Remote Similarity NPC474460
0.6731 Remote Similarity NPC59051
0.6731 Remote Similarity NPC182102
0.6727 Remote Similarity NPC54766
0.6727 Remote Similarity NPC473863
0.6727 Remote Similarity NPC152668
0.6727 Remote Similarity NPC45626
0.6727 Remote Similarity NPC274290
0.6724 Remote Similarity NPC471278
0.6667 Remote Similarity NPC213538
0.6667 Remote Similarity NPC67920
0.6667 Remote Similarity NPC298710
0.6667 Remote Similarity NPC256766
0.6667 Remote Similarity NPC287397
0.6667 Remote Similarity NPC151719
0.6667 Remote Similarity NPC474496
0.6667 Remote Similarity NPC217188
0.6667 Remote Similarity NPC470320
0.6667 Remote Similarity NPC196831
0.6667 Remote Similarity NPC174396
0.6667 Remote Similarity NPC226592
0.6667 Remote Similarity NPC329819
0.6604 Remote Similarity NPC244038
0.6604 Remote Similarity NPC261571
0.6604 Remote Similarity NPC28205
0.6604 Remote Similarity NPC284212
0.66 Remote Similarity NPC160628
0.66 Remote Similarity NPC239754
0.6591 Remote Similarity NPC58957
0.6552 Remote Similarity NPC326524
0.6552 Remote Similarity NPC473652
0.6552 Remote Similarity NPC329003
0.6552 Remote Similarity NPC325550
0.6545 Remote Similarity NPC137538
0.6545 Remote Similarity NPC269615
0.6538 Remote Similarity NPC98284
0.6538 Remote Similarity NPC207815
0.6531 Remote Similarity NPC269862
0.6491 Remote Similarity NPC225929
0.6491 Remote Similarity NPC474577
0.6481 Remote Similarity NPC92114
0.6481 Remote Similarity NPC35756
0.6481 Remote Similarity NPC129458
0.6481 Remote Similarity NPC188341
0.6481 Remote Similarity NPC49494
0.6471 Remote Similarity NPC44363
0.6471 Remote Similarity NPC110234
0.6471 Remote Similarity NPC42304
0.6471 Remote Similarity NPC163751
0.6458 Remote Similarity NPC188596

  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 NPC108195 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
0.6939 Remote Similarity NPD4265 Approved
0.66 Remote Similarity NPD39 Approved
0.6364 Remote Similarity NPD3172 Approved
0.6316 Remote Similarity NPD4219 Approved
0.6275 Remote Similarity NPD4222 Approved
0.625 Remote Similarity NPD3195 Phase 2
0.625 Remote Similarity NPD4266 Approved
0.625 Remote Similarity NPD3196 Approved
0.625 Remote Similarity NPD3194 Approved
0.623 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6226 Remote Similarity NPD3173 Approved
0.62 Remote Similarity NPD5326 Phase 3
0.6167 Remote Similarity NPD4246 Clinical (unspecified phase)
0.614 Remote Similarity NPD342 Phase 1
0.614 Remote Similarity NPD4627 Clinical (unspecified phase)
0.6129 Remote Similarity NPD3197 Phase 1
0.5778 Remote Similarity NPD2272 Approved
0.5778 Remote Similarity NPD5383 Approved
0.5769 Remote Similarity NPD6097 Approved
0.5769 Remote Similarity NPD6096 Approved
0.5741 Remote Similarity NPD5343 Approved
0.5714 Remote Similarity NPD29 Approved
0.5714 Remote Similarity NPD28 Approved
0.566 Remote Similarity NPD3174 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