Structure

Physi-Chem Properties

Molecular Weight:  214.14
Volume:  258.331
LogP:  3.444
LogD:  2.769
LogS:  -3.996
# Rotatable Bonds:  5
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.424
Synthetic Accessibility Score:  3.695
Fsp3:  0.333
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:  -3.807
MDCK Permeability:  7.622789416927844e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.08
20% Bioavailability (F20%):  0.09
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.004
Plasma Protein Binding (PPB):  100.34258270263672%
Volume Distribution (VD):  0.755
Pgp-substrate:  2.1158981323242188%

ADMET: Metabolism

CYP1A2-inhibitor:  0.97
CYP1A2-substrate:  0.251
CYP2C19-inhibitor:  0.964
CYP2C19-substrate:  0.624
CYP2C9-inhibitor:  0.898
CYP2C9-substrate:  0.966
CYP2D6-inhibitor:  0.924
CYP2D6-substrate:  0.87
CYP3A4-inhibitor:  0.93
CYP3A4-substrate:  0.254

ADMET: Excretion

Clearance (CL):  6.083
Half-life (T1/2):  0.402

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.926
Drug-inuced Liver Injury (DILI):  0.986
AMES Toxicity:  0.685
Rat Oral Acute Toxicity:  0.126
Maximum Recommended Daily Dose:  0.774
Skin Sensitization:  0.957
Carcinogencity:  0.601
Eye Corrosion:  0.971
Eye Irritation:  0.996
Respiratory Toxicity:  0.639

Download Data

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

  Natural Product: NPC206906

Natural Product ID:  NPC206906
Common Name*:   (2Z,8E,10E)-Pentadecatriene-4,6-Diyn-1-Ol
IUPAC Name:   (2Z,8E,10E)-pentadeca-2,8,10-trien-4,6-diyn-1-ol
Synonyms:  
Standard InCHIKey:  NEGOOEOCQZTKIT-INWOKVTFSA-N
Standard InCHI:  InChI=1S/C15H18O/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16/h5-8,13-14,16H,2-4,15H2,1H3/b6-5+,8-7+,14-13-
SMILES:  CCCC/C=C/C=C/C#CC#C/C=CCO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1092809
PubChem CID:   44613551
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
NPO16425 Bupleurum longiradiatum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[19994846]
NPO16425 Bupleurum longiradiatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16425 Bupleurum longiradiatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16425 Bupleurum longiradiatum 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
NPT116 Cell Line HL-60 Homo sapiens IC50 = 11000.0 nM PMID[513274]

☑ 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 NPC206906 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
0.907 High Similarity NPC180575
0.9024 High Similarity NPC304151
0.875 High Similarity NPC15934
0.8605 High Similarity NPC138935
0.8478 Intermediate Similarity NPC328784
0.8478 Intermediate Similarity NPC291437
0.8409 Intermediate Similarity NPC269074
0.8298 Intermediate Similarity NPC59408
0.8298 Intermediate Similarity NPC71053
0.8293 Intermediate Similarity NPC182840
0.8293 Intermediate Similarity NPC29091
0.8293 Intermediate Similarity NPC103213
0.8293 Intermediate Similarity NPC255042
0.8205 Intermediate Similarity NPC58957
0.8 Intermediate Similarity NPC276825
0.7959 Intermediate Similarity NPC61177
0.7949 Intermediate Similarity NPC250734
0.7907 Intermediate Similarity NPC269823
0.7872 Intermediate Similarity NPC31194
0.7872 Intermediate Similarity NPC85079
0.7872 Intermediate Similarity NPC153538
0.7872 Intermediate Similarity NPC248884
0.7826 Intermediate Similarity NPC124183
0.7826 Intermediate Similarity NPC55063
0.7826 Intermediate Similarity NPC19834
0.7826 Intermediate Similarity NPC35141
0.78 Intermediate Similarity NPC110732
0.7778 Intermediate Similarity NPC101616
0.7727 Intermediate Similarity NPC256766
0.7727 Intermediate Similarity NPC213538
0.7708 Intermediate Similarity NPC473913
0.7708 Intermediate Similarity NPC72699
0.7708 Intermediate Similarity NPC249670
0.7708 Intermediate Similarity NPC474642
0.7674 Intermediate Similarity NPC103236
0.7674 Intermediate Similarity NPC329762
0.7674 Intermediate Similarity NPC27444
0.7619 Intermediate Similarity NPC34873
0.7619 Intermediate Similarity NPC40434
0.76 Intermediate Similarity NPC34577
0.7556 Intermediate Similarity NPC116934
0.7551 Intermediate Similarity NPC151782
0.7551 Intermediate Similarity NPC93639
0.75 Intermediate Similarity NPC125122
0.75 Intermediate Similarity NPC302310
0.75 Intermediate Similarity NPC471276
0.75 Intermediate Similarity NPC471275
0.75 Intermediate Similarity NPC471280
0.74 Intermediate Similarity NPC142092
0.7391 Intermediate Similarity NPC108195
0.7358 Intermediate Similarity NPC44542
0.7358 Intermediate Similarity NPC472445
0.7347 Intermediate Similarity NPC471281
0.7347 Intermediate Similarity NPC199286
0.7347 Intermediate Similarity NPC477727
0.7333 Intermediate Similarity NPC149668
0.7234 Intermediate Similarity NPC160628
0.7234 Intermediate Similarity NPC140501
0.72 Intermediate Similarity NPC197272
0.72 Intermediate Similarity NPC89824
0.72 Intermediate Similarity NPC9273
0.72 Intermediate Similarity NPC477723
0.72 Intermediate Similarity NPC170776
0.72 Intermediate Similarity NPC165447
0.72 Intermediate Similarity NPC329608
0.72 Intermediate Similarity NPC294278
0.72 Intermediate Similarity NPC475477
0.72 Intermediate Similarity NPC224148
0.72 Intermediate Similarity NPC129263
0.72 Intermediate Similarity NPC76198
0.72 Intermediate Similarity NPC55383
0.72 Intermediate Similarity NPC471959
0.72 Intermediate Similarity NPC256656
0.7143 Intermediate Similarity NPC213767
0.7115 Intermediate Similarity NPC49059
0.7115 Intermediate Similarity NPC256209
0.7 Intermediate Similarity NPC474460
0.6981 Remote Similarity NPC474644
0.6977 Remote Similarity NPC216416
0.6923 Remote Similarity NPC284224
0.6852 Remote Similarity NPC249645
0.6852 Remote Similarity NPC472808
0.6852 Remote Similarity NPC324224
0.6852 Remote Similarity NPC55412
0.6852 Remote Similarity NPC473865
0.6852 Remote Similarity NPC474643
0.6829 Remote Similarity NPC63121
0.6829 Remote Similarity NPC197356
0.6809 Remote Similarity NPC252978
0.68 Remote Similarity NPC267110
0.6792 Remote Similarity NPC473532
0.6792 Remote Similarity NPC300121
0.6792 Remote Similarity NPC48058
0.6786 Remote Similarity NPC222852
0.6744 Remote Similarity NPC79544
0.6735 Remote Similarity NPC157096
0.6731 Remote Similarity NPC106531
0.6731 Remote Similarity NPC35756
0.6727 Remote Similarity NPC265551
0.6727 Remote Similarity NPC212730
0.6727 Remote Similarity NPC193975
0.6667 Remote Similarity NPC152668
0.6667 Remote Similarity NPC473735
0.6667 Remote Similarity NPC477725
0.6667 Remote Similarity NPC473910
0.6667 Remote Similarity NPC473725
0.6667 Remote Similarity NPC329686
0.6667 Remote Similarity NPC471991
0.6667 Remote Similarity NPC470963
0.6667 Remote Similarity NPC182102
0.6667 Remote Similarity NPC473896
0.6667 Remote Similarity NPC471239
0.6667 Remote Similarity NPC475071
0.6667 Remote Similarity NPC473721
0.6667 Remote Similarity NPC475353
0.6667 Remote Similarity NPC81989
0.6667 Remote Similarity NPC146551
0.6667 Remote Similarity NPC26960
0.6667 Remote Similarity NPC477726
0.6667 Remote Similarity NPC474513
0.6604 Remote Similarity NPC119655
0.6596 Remote Similarity NPC209279
0.6596 Remote Similarity NPC180871
0.6596 Remote Similarity NPC108494
0.6596 Remote Similarity NPC249801
0.6596 Remote Similarity NPC51758
0.6596 Remote Similarity NPC68889
0.6596 Remote Similarity NPC194586
0.6596 Remote Similarity NPC88079
0.6596 Remote Similarity NPC67761
0.6596 Remote Similarity NPC208936
0.6596 Remote Similarity NPC46248
0.6545 Remote Similarity NPC470966
0.6545 Remote Similarity NPC477661
0.6545 Remote Similarity NPC471960
0.6545 Remote Similarity NPC470968
0.6545 Remote Similarity NPC470969
0.6545 Remote Similarity NPC311648
0.6545 Remote Similarity NPC161838
0.6545 Remote Similarity NPC473847
0.6545 Remote Similarity NPC475384
0.6545 Remote Similarity NPC470964
0.6545 Remote Similarity NPC470967
0.6538 Remote Similarity NPC474495
0.6538 Remote Similarity NPC29234
0.6538 Remote Similarity NPC244038
0.6538 Remote Similarity NPC473672
0.6531 Remote Similarity NPC76976
0.6522 Remote Similarity NPC56917
0.6522 Remote Similarity NPC323278
0.6491 Remote Similarity NPC322002
0.6491 Remote Similarity NPC318306
0.6491 Remote Similarity NPC322186
0.6481 Remote Similarity NPC123669
0.6481 Remote Similarity NPC167759
0.6481 Remote Similarity NPC305288
0.6481 Remote Similarity NPC56028
0.6481 Remote Similarity NPC269615
0.6481 Remote Similarity NPC163912
0.6429 Remote Similarity NPC470970
0.6429 Remote Similarity NPC594
0.6429 Remote Similarity NPC48968
0.6415 Remote Similarity NPC208638
0.6415 Remote Similarity NPC195986
0.6383 Remote Similarity NPC469713
0.6379 Remote Similarity NPC471278
0.6379 Remote Similarity NPC327112
0.6364 Remote Similarity NPC317899
0.6364 Remote Similarity NPC474913
0.6346 Remote Similarity NPC307435
0.6346 Remote Similarity NPC473768
0.6346 Remote Similarity NPC267692
0.6341 Remote Similarity NPC60288
0.6341 Remote Similarity NPC242117
0.6327 Remote Similarity NPC304079
0.6327 Remote Similarity NPC6963
0.6316 Remote Similarity NPC469373
0.6304 Remote Similarity NPC306850
0.6304 Remote Similarity NPC277382
0.6304 Remote Similarity NPC171978
0.6296 Remote Similarity NPC303672
0.6296 Remote Similarity NPC474496
0.6275 Remote Similarity NPC91044
0.6271 Remote Similarity NPC325929
0.6271 Remote Similarity NPC66460
0.6271 Remote Similarity NPC271282
0.625 Remote Similarity NPC477049
0.625 Remote Similarity NPC31121
0.6226 Remote Similarity NPC54542
0.6226 Remote Similarity NPC243539
0.6226 Remote Similarity NPC267340
0.6226 Remote Similarity NPC145032
0.6226 Remote Similarity NPC304223
0.6207 Remote Similarity NPC473652
0.62 Remote Similarity NPC210560
0.62 Remote Similarity NPC474202
0.62 Remote Similarity NPC474362
0.62 Remote Similarity NPC221379
0.62 Remote Similarity NPC24824
0.62 Remote Similarity NPC165651

  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 NPC206906 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
0.7234 Intermediate Similarity NPD4265 Approved
0.6852 Remote Similarity NPD4219 Approved
0.68 Remote Similarity NPD4220 Pre-registration
0.6379 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6071 Remote Similarity NPD342 Phase 1
0.6034 Remote Similarity NPD585 Clinical (unspecified phase)
0.5781 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5741 Remote Similarity NPD2268 Discontinued
0.5645 Remote Similarity NPD3210 Clinical (unspecified phase)

  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