Structure

Physi-Chem Properties

Molecular Weight:  180.08
Volume:  194.705
LogP:  0.593
LogD:  0.058
LogS:  -0.926
# Rotatable Bonds:  3
TPSA:  60.69
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.397
Synthetic Accessibility Score:  4.609
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:  -5.214
MDCK Permeability:  0.0016597127541899681
Pgp-inhibitor:  0.002
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.663
20% Bioavailability (F20%):  0.81
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.391
Plasma Protein Binding (PPB):  94.90206146240234%
Volume Distribution (VD):  0.735
Pgp-substrate:  4.612087249755859%

ADMET: Metabolism

CYP1A2-inhibitor:  0.032
CYP1A2-substrate:  0.053
CYP2C19-inhibitor:  0.619
CYP2C19-substrate:  0.515
CYP2C9-inhibitor:  0.797
CYP2C9-substrate:  0.933
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.128
CYP3A4-inhibitor:  0.3
CYP3A4-substrate:  0.121

ADMET: Excretion

Clearance (CL):  4.317
Half-life (T1/2):  0.731

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.149
Drug-inuced Liver Injury (DILI):  0.952
AMES Toxicity:  0.962
Rat Oral Acute Toxicity:  0.997
Maximum Recommended Daily Dose:  0.999
Skin Sensitization:  0.943
Carcinogencity:  0.097
Eye Corrosion:  0.939
Eye Irritation:  0.991
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: NPC306850

Natural Product ID:  NPC306850
Common Name*:   1,3R,8R-Trihydroxydec-9-En-4,6-Yne
IUPAC Name:   (3R,8R)-dec-9-en-4,6-diyne-1,3,8-triol
Synonyms:  
Standard InCHIKey:  HCTNZAAVSRVKLJ-ZJUUUORDSA-N
Standard InCHI:  InChI=1S/C10H12O3/c1-2-9(12)5-3-4-6-10(13)7-8-11/h2,9-13H,1,7-8H2/t9-,10+/m1/s1
SMILES:  OCC[C@H](C#CC#C[C@@H](C=C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL470664
PubChem CID:   10261702
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
NPO25496 Artemisia monosperma Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[15165159]
NPO25496 Artemisia monosperma Species Asteraceae Eukaryota n.a. stem n.a. PMID[22978234]
NPO25496 Artemisia monosperma Species Asteraceae Eukaryota n.a. leaf n.a. PMID[22978234]
NPO25496 Artemisia monosperma Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]

☑ 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 128.0 ug.mL-1 PMID[528447]

☑ 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 NPC306850 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 NPC174396
0.7692 Intermediate Similarity NPC79544
0.7632 Intermediate Similarity NPC81989
0.7447 Intermediate Similarity NPC328784
0.7447 Intermediate Similarity NPC291437
0.7292 Intermediate Similarity NPC151782
0.7234 Intermediate Similarity NPC153538
0.7174 Intermediate Similarity NPC35141
0.7174 Intermediate Similarity NPC124183
0.7111 Intermediate Similarity NPC101616
0.7083 Intermediate Similarity NPC72699
0.7045 Intermediate Similarity NPC249801
0.7045 Intermediate Similarity NPC46248
0.6939 Remote Similarity NPC59408
0.6939 Remote Similarity NPC71053
0.6939 Remote Similarity NPC93639
0.6875 Remote Similarity NPC471280
0.6875 Remote Similarity NPC125122
0.6875 Remote Similarity NPC248884
0.6875 Remote Similarity NPC471276
0.6875 Remote Similarity NPC471275
0.6875 Remote Similarity NPC85079
0.6875 Remote Similarity NPC302310
0.6875 Remote Similarity NPC31194
0.6863 Remote Similarity NPC110732
0.6863 Remote Similarity NPC473532
0.6863 Remote Similarity NPC49059
0.6863 Remote Similarity NPC256209
0.6829 Remote Similarity NPC213767
0.6809 Remote Similarity NPC19834
0.6809 Remote Similarity NPC157096
0.6809 Remote Similarity NPC55063
0.6792 Remote Similarity NPC474577
0.6735 Remote Similarity NPC471281
0.6735 Remote Similarity NPC199286
0.6735 Remote Similarity NPC473487
0.6735 Remote Similarity NPC477727
0.6731 Remote Similarity NPC473910
0.6731 Remote Similarity NPC473725
0.6731 Remote Similarity NPC477726
0.6731 Remote Similarity NPC473721
0.6731 Remote Similarity NPC473896
0.6731 Remote Similarity NPC477725
0.6731 Remote Similarity NPC473735
0.6731 Remote Similarity NPC475353
0.6667 Remote Similarity NPC304151
0.6667 Remote Similarity NPC216416
0.6604 Remote Similarity NPC470969
0.6604 Remote Similarity NPC471960
0.6604 Remote Similarity NPC161838
0.6604 Remote Similarity NPC477661
0.6604 Remote Similarity NPC470966
0.6604 Remote Similarity NPC470968
0.6604 Remote Similarity NPC470967
0.6604 Remote Similarity NPC473847
0.6604 Remote Similarity NPC475384
0.66 Remote Similarity NPC165447
0.66 Remote Similarity NPC477723
0.66 Remote Similarity NPC197272
0.66 Remote Similarity NPC170776
0.66 Remote Similarity NPC329608
0.66 Remote Similarity NPC76198
0.66 Remote Similarity NPC9273
0.66 Remote Similarity NPC475477
0.66 Remote Similarity NPC471959
0.66 Remote Similarity NPC256656
0.66 Remote Similarity NPC55383
0.66 Remote Similarity NPC294278
0.66 Remote Similarity NPC129263
0.66 Remote Similarity NPC89824
0.66 Remote Similarity NPC224148
0.6531 Remote Similarity NPC475153
0.6481 Remote Similarity NPC472445
0.6481 Remote Similarity NPC470970
0.6471 Remote Similarity NPC142092
0.6471 Remote Similarity NPC473705
0.6444 Remote Similarity NPC473625
0.64 Remote Similarity NPC473768
0.64 Remote Similarity NPC473913
0.64 Remote Similarity NPC474642
0.64 Remote Similarity NPC249670
0.6383 Remote Similarity NPC108195
0.6346 Remote Similarity NPC26102
0.6346 Remote Similarity NPC477724
0.6346 Remote Similarity NPC34577
0.6346 Remote Similarity NPC187361
0.6341 Remote Similarity NPC250734
0.6304 Remote Similarity NPC31121
0.6304 Remote Similarity NPC206906
0.6275 Remote Similarity NPC200772
0.6275 Remote Similarity NPC29234
0.625 Remote Similarity NPC201948
0.625 Remote Similarity NPC276825
0.625 Remote Similarity NPC269074
0.6226 Remote Similarity NPC48058
0.6222 Remote Similarity NPC103236
0.6222 Remote Similarity NPC27444
0.6222 Remote Similarity NPC329762
0.619 Remote Similarity NPC58957
0.6182 Remote Similarity NPC193975
0.6154 Remote Similarity NPC35756
0.6136 Remote Similarity NPC34873
0.6136 Remote Similarity NPC40434
0.6122 Remote Similarity NPC180575
0.6111 Remote Similarity NPC474513
0.6111 Remote Similarity NPC471239
0.6111 Remote Similarity NPC470963
0.6111 Remote Similarity NPC152668
0.6111 Remote Similarity NPC146551
0.6111 Remote Similarity NPC306009
0.6098 Remote Similarity NPC197356
0.6098 Remote Similarity NPC63121
0.6078 Remote Similarity NPC474460
0.6042 Remote Similarity NPC474413
0.6042 Remote Similarity NPC473539
0.6038 Remote Similarity NPC284224
0.6038 Remote Similarity NPC474496
0.6034 Remote Similarity NPC475984
0.6 Remote Similarity NPC28077
0.6 Remote Similarity NPC311648
0.6 Remote Similarity NPC15934
0.6 Remote Similarity NPC470964
0.5962 Remote Similarity NPC470411
0.5962 Remote Similarity NPC473672
0.5962 Remote Similarity NPC474495
0.5957 Remote Similarity NPC149668
0.5946 Remote Similarity NPC88887
0.5932 Remote Similarity NPC29697
0.5932 Remote Similarity NPC470965
0.5926 Remote Similarity NPC300121
0.5918 Remote Similarity NPC160628
0.5918 Remote Similarity NPC140501
0.5893 Remote Similarity NPC212730
0.5893 Remote Similarity NPC48968
0.5893 Remote Similarity NPC594
0.5893 Remote Similarity NPC265551
0.5893 Remote Similarity NPC44542
0.5833 Remote Similarity NPC226592
0.5833 Remote Similarity NPC116934
0.5818 Remote Similarity NPC474644
0.5818 Remote Similarity NPC227135
0.5818 Remote Similarity NPC317899
0.5789 Remote Similarity NPC181872
0.5763 Remote Similarity NPC325929
0.5763 Remote Similarity NPC66460
0.5763 Remote Similarity NPC477829
0.5763 Remote Similarity NPC271282
0.5741 Remote Similarity NPC61177
0.5741 Remote Similarity NPC217188
0.5741 Remote Similarity NPC475723
0.5714 Remote Similarity NPC324224
0.5714 Remote Similarity NPC474643
0.5714 Remote Similarity NPC473865
0.5714 Remote Similarity NPC472808
0.569 Remote Similarity NPC473652
0.569 Remote Similarity NPC97570
0.569 Remote Similarity NPC222852
0.569 Remote Similarity NPC318306
0.5652 Remote Similarity NPC29091
0.5652 Remote Similarity NPC103213
0.5652 Remote Similarity NPC182840
0.5652 Remote Similarity NPC255042
0.5641 Remote Similarity NPC320326
0.5625 Remote Similarity NPC194586
0.5625 Remote Similarity NPC88079
0.5625 Remote Similarity NPC67761
0.5625 Remote Similarity NPC209279
0.5625 Remote Similarity NPC108494
0.5625 Remote Similarity NPC68889
0.5625 Remote Similarity NPC51758
0.5625 Remote Similarity NPC180871
0.5614 Remote Similarity NPC71755
0.5614 Remote Similarity NPC121034
0.561 Remote Similarity NPC242117

  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 NPC306850 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
0.5918 Remote Similarity NPD4265 Approved
0.5789 Remote Similarity NPD585 Clinical (unspecified phase)
0.5745 Remote Similarity NPD9301 Approved
0.5745 Remote Similarity NPD9300 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