Structure

Physi-Chem Properties

Molecular Weight:  260.18
Volume:  304.35
LogP:  3.411
LogD:  3.007
LogS:  -4.018
# 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:  0.4
Synthetic Accessibility Score:  3.751
Fsp3:  0.529
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:  -3.884
MDCK Permeability:  3.4127682738471776e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.101
20% Bioavailability (F20%):  0.88
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.024
Plasma Protein Binding (PPB):  98.9116439819336%
Volume Distribution (VD):  1.054
Pgp-substrate:  1.926292896270752%

ADMET: Metabolism

CYP1A2-inhibitor:  0.906
CYP1A2-substrate:  0.24
CYP2C19-inhibitor:  0.95
CYP2C19-substrate:  0.718
CYP2C9-inhibitor:  0.889
CYP2C9-substrate:  0.992
CYP2D6-inhibitor:  0.874
CYP2D6-substrate:  0.903
CYP3A4-inhibitor:  0.922
CYP3A4-substrate:  0.211

ADMET: Excretion

Clearance (CL):  9.246
Half-life (T1/2):  0.27

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.779
Drug-inuced Liver Injury (DILI):  0.965
AMES Toxicity:  0.541
Rat Oral Acute Toxicity:  0.157
Maximum Recommended Daily Dose:  0.536
Skin Sensitization:  0.951
Carcinogencity:  0.843
Eye Corrosion:  0.964
Eye Irritation:  0.987
Respiratory Toxicity:  0.916

Download Data

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

  Natural Product: NPC110732

Natural Product ID:  NPC110732
Common Name*:   Heptadeca-8,10-Diene-4,6-Diyne-1,12-Diol
IUPAC Name:   (8E,10E,12S)-heptadeca-8,10-dien-4,6-diyne-1,12-diol
Synonyms:  
Standard InCHIKey:  UYZBGAFJAALREV-WHLLTAFYSA-N
Standard InCHI:  InChI=1S/C17H24O2/c1-2-3-11-14-17(19)15-12-9-7-5-4-6-8-10-13-16-18/h7,9,12,15,17-19H,2-3,10-11,13-14,16H2,1H3/b9-7+,15-12+/t17-/m0/s1
SMILES:  CCCCC[C@@H](/C=C/C=C/C#CC#CCCCO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL423178
PubChem CID:   11108083
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 = 9.5 mg kg-1 i.p. PMID[534211]
NPT805 Protein Complex GABA-A receptor; anion channel Rattus norvegicus IC50 = 1150.0 nM PMID[534211]

☑ 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 NPC110732 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
0.94 High Similarity NPC71053
0.94 High Similarity NPC59408
0.9231 High Similarity NPC256209
0.9231 High Similarity NPC49059
0.92 High Similarity NPC291437
0.92 High Similarity NPC328784
0.9038 High Similarity NPC34577
0.902 High Similarity NPC151782
0.9 High Similarity NPC302310
0.9 High Similarity NPC153538
0.8824 High Similarity NPC72699
0.8704 High Similarity NPC473910
0.8704 High Similarity NPC473721
0.8704 High Similarity NPC473735
0.8704 High Similarity NPC477725
0.8704 High Similarity NPC473725
0.8704 High Similarity NPC477726
0.8704 High Similarity NPC475353
0.8704 High Similarity NPC473896
0.8654 High Similarity NPC129263
0.8654 High Similarity NPC93639
0.8627 High Similarity NPC31194
0.8627 High Similarity NPC248884
0.8627 High Similarity NPC85079
0.86 High Similarity NPC35141
0.86 High Similarity NPC180575
0.86 High Similarity NPC124183
0.8545 High Similarity NPC470969
0.8545 High Similarity NPC470968
0.8545 High Similarity NPC161838
0.8545 High Similarity NPC471960
0.8545 High Similarity NPC470967
0.8545 High Similarity NPC473847
0.8545 High Similarity NPC477661
0.8545 High Similarity NPC470966
0.8545 High Similarity NPC475384
0.8519 High Similarity NPC473532
0.84 Intermediate Similarity NPC276825
0.8393 Intermediate Similarity NPC470970
0.8269 Intermediate Similarity NPC125122
0.8269 Intermediate Similarity NPC471275
0.8269 Intermediate Similarity NPC471280
0.8269 Intermediate Similarity NPC471276
0.8235 Intermediate Similarity NPC55063
0.8235 Intermediate Similarity NPC19834
0.82 Intermediate Similarity NPC101616
0.8148 Intermediate Similarity NPC142092
0.8113 Intermediate Similarity NPC477727
0.8113 Intermediate Similarity NPC471281
0.8113 Intermediate Similarity NPC249670
0.8113 Intermediate Similarity NPC474642
0.8113 Intermediate Similarity NPC473913
0.8113 Intermediate Similarity NPC199286
0.807 Intermediate Similarity NPC44542
0.807 Intermediate Similarity NPC472445
0.8039 Intermediate Similarity NPC269074
0.8 Intermediate Similarity NPC187361
0.8 Intermediate Similarity NPC61177
0.8 Intermediate Similarity NPC284224
0.8 Intermediate Similarity NPC474496
0.8 Intermediate Similarity NPC26102
0.8 Intermediate Similarity NPC29697
0.8 Intermediate Similarity NPC477724
0.7966 Intermediate Similarity NPC327112
0.7963 Intermediate Similarity NPC474495
0.7963 Intermediate Similarity NPC473672
0.7963 Intermediate Similarity NPC471959
0.7963 Intermediate Similarity NPC224148
0.7963 Intermediate Similarity NPC294278
0.7963 Intermediate Similarity NPC55383
0.7963 Intermediate Similarity NPC89824
0.7963 Intermediate Similarity NPC256656
0.7963 Intermediate Similarity NPC329608
0.7963 Intermediate Similarity NPC9273
0.7963 Intermediate Similarity NPC475477
0.7963 Intermediate Similarity NPC165447
0.7963 Intermediate Similarity NPC170776
0.7963 Intermediate Similarity NPC76198
0.7963 Intermediate Similarity NPC197272
0.7963 Intermediate Similarity NPC477723
0.7843 Intermediate Similarity NPC108195
0.7833 Intermediate Similarity NPC325929
0.7833 Intermediate Similarity NPC66460
0.7833 Intermediate Similarity NPC271282
0.7833 Intermediate Similarity NPC475984
0.78 Intermediate Similarity NPC206906
0.78 Intermediate Similarity NPC249801
0.78 Intermediate Similarity NPC304151
0.78 Intermediate Similarity NPC46248
0.7797 Intermediate Similarity NPC222852
0.7759 Intermediate Similarity NPC193975
0.7719 Intermediate Similarity NPC317899
0.7705 Intermediate Similarity NPC470965
0.7586 Intermediate Similarity NPC324224
0.7586 Intermediate Similarity NPC472808
0.7581 Intermediate Similarity NPC226592
0.7581 Intermediate Similarity NPC470320
0.7547 Intermediate Similarity NPC157096
0.7544 Intermediate Similarity NPC48058
0.746 Intermediate Similarity NPC245947
0.746 Intermediate Similarity NPC255863
0.746 Intermediate Similarity NPC308844
0.746 Intermediate Similarity NPC136164
0.7458 Intermediate Similarity NPC212730
0.7458 Intermediate Similarity NPC265551
0.7414 Intermediate Similarity NPC470963
0.7414 Intermediate Similarity NPC227135
0.7414 Intermediate Similarity NPC474513
0.7414 Intermediate Similarity NPC474644
0.7414 Intermediate Similarity NPC146551
0.7414 Intermediate Similarity NPC329686
0.7414 Intermediate Similarity NPC152668
0.7414 Intermediate Similarity NPC471239
0.7377 Intermediate Similarity NPC328311
0.7368 Intermediate Similarity NPC217188
0.7358 Intermediate Similarity NPC140501
0.7358 Intermediate Similarity NPC76976
0.7333 Intermediate Similarity NPC469373
0.7333 Intermediate Similarity NPC226848
0.7308 Intermediate Similarity NPC252978
0.7288 Intermediate Similarity NPC311648
0.7288 Intermediate Similarity NPC473865
0.7288 Intermediate Similarity NPC470964
0.7288 Intermediate Similarity NPC474643
0.7258 Intermediate Similarity NPC477829
0.7241 Intermediate Similarity NPC300121
0.7213 Intermediate Similarity NPC322002
0.7213 Intermediate Similarity NPC122239
0.7213 Intermediate Similarity NPC475931
0.7213 Intermediate Similarity NPC318306
0.72 Intermediate Similarity NPC15934
0.7193 Intermediate Similarity NPC35756
0.7188 Intermediate Similarity NPC317881
0.7188 Intermediate Similarity NPC323045
0.717 Intermediate Similarity NPC138935
0.7167 Intermediate Similarity NPC474577
0.7167 Intermediate Similarity NPC594
0.7167 Intermediate Similarity NPC48968
0.7143 Intermediate Similarity NPC474460
0.7143 Intermediate Similarity NPC473768
0.7115 Intermediate Similarity NPC149668
0.7097 Intermediate Similarity NPC471278
0.7059 Intermediate Similarity NPC329762
0.7059 Intermediate Similarity NPC103236
0.7059 Intermediate Similarity NPC27444
0.7049 Intermediate Similarity NPC181872
0.7049 Intermediate Similarity NPC155025
0.7018 Intermediate Similarity NPC29234
0.7015 Intermediate Similarity NPC143396
0.7015 Intermediate Similarity NPC236208
0.7 Intermediate Similarity NPC40434
0.7 Intermediate Similarity NPC34873
0.7 Intermediate Similarity NPC48891
0.6984 Remote Similarity NPC113293
0.6984 Remote Similarity NPC225342
0.6981 Remote Similarity NPC116934
0.697 Remote Similarity NPC473752
0.697 Remote Similarity NPC49863
0.6935 Remote Similarity NPC322186
0.6935 Remote Similarity NPC329249
0.6935 Remote Similarity NPC473652
0.6935 Remote Similarity NPC474267
0.6923 Remote Similarity NPC323477
0.6923 Remote Similarity NPC326268
0.6923 Remote Similarity NPC318420
0.6912 Remote Similarity NPC476037
0.6897 Remote Similarity NPC473705
0.6863 Remote Similarity NPC306850
0.6842 Remote Similarity NPC288381
0.6842 Remote Similarity NPC473487
0.6842 Remote Similarity NPC20934
0.6833 Remote Similarity NPC281590
0.6833 Remote Similarity NPC474913
0.6833 Remote Similarity NPC251666
0.6833 Remote Similarity NPC232247
0.6825 Remote Similarity NPC99487
0.6825 Remote Similarity NPC299730
0.6818 Remote Similarity NPC146811
0.6818 Remote Similarity NPC328653
0.6812 Remote Similarity NPC95863
0.6769 Remote Similarity NPC300593
0.6769 Remote Similarity NPC110241
0.6765 Remote Similarity NPC239373
0.6765 Remote Similarity NPC329989
0.6727 Remote Similarity NPC160628
0.6724 Remote Similarity NPC200772
0.6719 Remote Similarity NPC68679
0.6719 Remote Similarity NPC168407
0.6719 Remote Similarity NPC207007
0.6719 Remote Similarity NPC26810
0.6719 Remote Similarity NPC321867
0.6716 Remote Similarity NPC26500
0.6716 Remote Similarity NPC73603
0.6716 Remote Similarity NPC99619
0.6714 Remote Similarity NPC329890
0.6714 Remote Similarity NPC325627
0.6667 Remote Similarity NPC269615
0.6667 Remote Similarity NPC475153
0.6667 Remote Similarity NPC267110
0.6667 Remote Similarity NPC476012

  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 NPC110732 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
0.7966 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.7358 Intermediate Similarity NPD4265 Approved
0.697 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6719 Remote Similarity NPD368 Approved
0.6714 Remote Similarity NPD4732 Discontinued
0.6615 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6557 Remote Similarity NPD342 Phase 1
0.6528 Remote Similarity NPD8264 Approved
0.6452 Remote Similarity NPD4219 Approved
0.6269 Remote Similarity NPD3197 Phase 1
0.6267 Remote Similarity NPD7322 Clinical (unspecified phase)
0.625 Remote Similarity NPD585 Clinical (unspecified phase)
0.6234 Remote Similarity NPD6898 Phase 1
0.6104 Remote Similarity NPD7332 Phase 2
0.6104 Remote Similarity NPD7514 Phase 3
0.6102 Remote Similarity NPD4220 Pre-registration
0.6102 Remote Similarity NPD3173 Approved
0.6076 Remote Similarity NPD5331 Approved
0.6076 Remote Similarity NPD5332 Approved
0.6053 Remote Similarity NPD7145 Approved
0.6026 Remote Similarity NPD6902 Approved
0.5974 Remote Similarity NPD6683 Phase 2
0.5972 Remote Similarity NPD3212 Clinical (unspecified phase)
0.5972 Remote Similarity NPD7143 Approved
0.5972 Remote Similarity NPD7144 Approved
0.5968 Remote Similarity NPD3172 Approved
0.5921 Remote Similarity NPD5776 Phase 2
0.5921 Remote Similarity NPD6925 Approved
0.589 Remote Similarity NPD7151 Approved
0.589 Remote Similarity NPD7152 Approved
0.589 Remote Similarity NPD7150 Approved
0.5873 Remote Similarity NPD4266 Approved
0.5873 Remote Similarity NPD3195 Phase 2
0.5873 Remote Similarity NPD3196 Approved
0.5873 Remote Similarity NPD3194 Approved
0.5862 Remote Similarity NPD39 Approved
0.5862 Remote Similarity NPD4222 Approved
0.5844 Remote Similarity NPD4268 Approved
0.5844 Remote Similarity NPD4271 Approved
0.5844 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6922 Approved
0.5833 Remote Similarity NPD6923 Approved
0.5783 Remote Similarity NPD7750 Discontinued
0.5769 Remote Similarity NPD6929 Approved
0.5758 Remote Similarity NPD6109 Phase 1
0.5733 Remote Similarity NPD6926 Approved
0.5733 Remote Similarity NPD6924 Approved
0.5714 Remote Similarity NPD6932 Approved
0.5696 Remote Similarity NPD4819 Approved
0.5696 Remote Similarity NPD4822 Approved
0.5696 Remote Similarity NPD6930 Phase 2
0.5696 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5696 Remote Similarity NPD6931 Approved
0.5696 Remote Similarity NPD4821 Approved
0.5696 Remote Similarity NPD4820 Approved
0.5696 Remote Similarity NPD4252 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