Structure

Physi-Chem Properties

Molecular Weight:  260.18
Volume:  304.35
LogP:  3.787
LogD:  3.282
LogS:  -3.917
# 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:  3.841
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:  -4.441
MDCK Permeability:  6.065298293833621e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.231
20% Bioavailability (F20%):  0.998
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.024
Plasma Protein Binding (PPB):  100.40171813964844%
Volume Distribution (VD):  1.233
Pgp-substrate:  2.0602967739105225%

ADMET: Metabolism

CYP1A2-inhibitor:  0.913
CYP1A2-substrate:  0.288
CYP2C19-inhibitor:  0.925
CYP2C19-substrate:  0.58
CYP2C9-inhibitor:  0.824
CYP2C9-substrate:  0.892
CYP2D6-inhibitor:  0.264
CYP2D6-substrate:  0.071
CYP3A4-inhibitor:  0.915
CYP3A4-substrate:  0.208

ADMET: Excretion

Clearance (CL):  9.211
Half-life (T1/2):  0.887

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.935
Drug-inuced Liver Injury (DILI):  0.978
AMES Toxicity:  0.812
Rat Oral Acute Toxicity:  0.973
Maximum Recommended Daily Dose:  0.996
Skin Sensitization:  0.96
Carcinogencity:  0.336
Eye Corrosion:  0.962
Eye Irritation:  0.991
Respiratory Toxicity:  0.973

Download Data

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

  Natural Product: NPC85079

Natural Product ID:  NPC85079
Common Name*:   8S-Heptadeca-2(Z),9(Z)-Diene-4,6-Diyne-1,8-Diol
IUPAC Name:   (2Z,8S,9Z)-heptadeca-2,9-dien-4,6-diyne-1,8-diol
Synonyms:  
Standard InCHIKey:  UECWLXACMXYTFN-HVIKZBMUSA-N
Standard InCHI:  InChI=1S/C17H24O2/c1-2-3-4-5-6-8-11-14-17(19)15-12-9-7-10-13-16-18/h10-11,13-14,17-19H,2-6,8,16H2,1H3/b13-10-,14-11-/t17-/m0/s1
SMILES:  CCCCCCC/C=C[C@@H](C#CC#C/C=CCO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL463984
PubChem CID:   10400397
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
NPO11237 Bupleurum salicifolium Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24242108]
NPO11237 Bupleurum salicifolium Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[7964800]
NPO11237 Bupleurum salicifolium 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 10.0 ug.mL-1 PMID[464301]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 10.5 ug.mL-1 PMID[464301]

☑ 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 NPC85079 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 NPC248884
1.0 High Similarity NPC31194
0.9783 High Similarity NPC72699
0.9574 High Similarity NPC151782
0.9565 High Similarity NPC125122
0.9565 High Similarity NPC471276
0.9565 High Similarity NPC471275
0.9565 High Similarity NPC471280
0.9565 High Similarity NPC153538
0.9556 High Similarity NPC124183
0.9556 High Similarity NPC55063
0.9556 High Similarity NPC35141
0.9556 High Similarity NPC19834
0.9362 High Similarity NPC473913
0.9362 High Similarity NPC474642
0.9362 High Similarity NPC471281
0.9362 High Similarity NPC199286
0.9362 High Similarity NPC477727
0.9362 High Similarity NPC249670
0.9333 High Similarity NPC269074
0.9167 High Similarity NPC329608
0.9167 High Similarity NPC165447
0.9167 High Similarity NPC294278
0.9167 High Similarity NPC76198
0.9167 High Similarity NPC9273
0.9167 High Similarity NPC89824
0.9167 High Similarity NPC224148
0.9167 High Similarity NPC197272
0.9167 High Similarity NPC471959
0.9167 High Similarity NPC256656
0.9167 High Similarity NPC477723
0.9167 High Similarity NPC475477
0.9167 High Similarity NPC93639
0.9167 High Similarity NPC55383
0.9167 High Similarity NPC170776
0.9111 High Similarity NPC101616
0.9 High Similarity NPC256209
0.9 High Similarity NPC49059
0.898 High Similarity NPC142092
0.8776 High Similarity NPC71053
0.8776 High Similarity NPC59408
0.8723 High Similarity NPC180575
0.8667 High Similarity NPC304151
0.8627 High Similarity NPC110732
0.8627 High Similarity NPC48058
0.8627 High Similarity NPC473532
0.8571 High Similarity NPC328784
0.8571 High Similarity NPC291437
0.8491 Intermediate Similarity NPC193975
0.8462 Intermediate Similarity NPC473910
0.8462 Intermediate Similarity NPC477726
0.8462 Intermediate Similarity NPC473721
0.8462 Intermediate Similarity NPC474644
0.8462 Intermediate Similarity NPC475353
0.8462 Intermediate Similarity NPC474513
0.8462 Intermediate Similarity NPC473725
0.8462 Intermediate Similarity NPC477725
0.8462 Intermediate Similarity NPC473896
0.8462 Intermediate Similarity NPC473735
0.8462 Intermediate Similarity NPC471239
0.8462 Intermediate Similarity NPC146551
0.8462 Intermediate Similarity NPC470963
0.84 Intermediate Similarity NPC129263
0.8367 Intermediate Similarity NPC302310
0.8302 Intermediate Similarity NPC470964
0.8302 Intermediate Similarity NPC477661
0.8302 Intermediate Similarity NPC161838
0.8302 Intermediate Similarity NPC471960
0.8302 Intermediate Similarity NPC473865
0.8302 Intermediate Similarity NPC474643
0.8302 Intermediate Similarity NPC470967
0.8302 Intermediate Similarity NPC475384
0.8302 Intermediate Similarity NPC470966
0.8302 Intermediate Similarity NPC470969
0.8302 Intermediate Similarity NPC473847
0.8302 Intermediate Similarity NPC311648
0.8302 Intermediate Similarity NPC470968
0.8298 Intermediate Similarity NPC108195
0.8261 Intermediate Similarity NPC149668
0.8148 Intermediate Similarity NPC48968
0.8148 Intermediate Similarity NPC212730
0.8148 Intermediate Similarity NPC594
0.8148 Intermediate Similarity NPC265551
0.8148 Intermediate Similarity NPC470970
0.8113 Intermediate Similarity NPC152668
0.8077 Intermediate Similarity NPC34577
0.8077 Intermediate Similarity NPC61177
0.8039 Intermediate Similarity NPC474495
0.8039 Intermediate Similarity NPC473672
0.8036 Intermediate Similarity NPC471278
0.8 Intermediate Similarity NPC15934
0.7959 Intermediate Similarity NPC157096
0.7895 Intermediate Similarity NPC66460
0.7895 Intermediate Similarity NPC271282
0.7895 Intermediate Similarity NPC325929
0.7872 Intermediate Similarity NPC206906
0.7857 Intermediate Similarity NPC473652
0.7826 Intermediate Similarity NPC27444
0.7826 Intermediate Similarity NPC329762
0.7826 Intermediate Similarity NPC103236
0.7818 Intermediate Similarity NPC44542
0.7759 Intermediate Similarity NPC29697
0.7755 Intermediate Similarity NPC276825
0.7736 Intermediate Similarity NPC477724
0.7736 Intermediate Similarity NPC26102
0.7736 Intermediate Similarity NPC187361
0.7586 Intermediate Similarity NPC168407
0.7586 Intermediate Similarity NPC475984
0.7556 Intermediate Similarity NPC216416
0.75 Intermediate Similarity NPC472445
0.75 Intermediate Similarity NPC473768
0.75 Intermediate Similarity NPC475071
0.7458 Intermediate Similarity NPC470965
0.7407 Intermediate Similarity NPC474496
0.7407 Intermediate Similarity NPC284224
0.7358 Intermediate Similarity NPC29234
0.7347 Intermediate Similarity NPC116934
0.7333 Intermediate Similarity NPC226592
0.7333 Intermediate Similarity NPC470320
0.7333 Intermediate Similarity NPC213767
0.7308 Intermediate Similarity NPC475153
0.7292 Intermediate Similarity NPC269823
0.7241 Intermediate Similarity NPC222852
0.7234 Intermediate Similarity NPC255042
0.7234 Intermediate Similarity NPC182840
0.7234 Intermediate Similarity NPC29091
0.7234 Intermediate Similarity NPC103213
0.7222 Intermediate Similarity NPC35756
0.7222 Intermediate Similarity NPC473705
0.72 Intermediate Similarity NPC138935
0.7193 Intermediate Similarity NPC471277
0.7193 Intermediate Similarity NPC471279
0.717 Intermediate Similarity NPC474460
0.717 Intermediate Similarity NPC182102
0.717 Intermediate Similarity NPC26960
0.7143 Intermediate Similarity NPC317899
0.7143 Intermediate Similarity NPC256766
0.7143 Intermediate Similarity NPC213538
0.7143 Intermediate Similarity NPC46248
0.7143 Intermediate Similarity NPC249801
0.7111 Intermediate Similarity NPC58957
0.7091 Intermediate Similarity NPC217188
0.7069 Intermediate Similarity NPC181872
0.7059 Intermediate Similarity NPC474362
0.7059 Intermediate Similarity NPC474202
0.7059 Intermediate Similarity NPC160628
0.7059 Intermediate Similarity NPC76976
0.7059 Intermediate Similarity NPC140501
0.7 Intermediate Similarity NPC252978
0.6984 Remote Similarity NPC473752
0.6981 Remote Similarity NPC267110
0.6964 Remote Similarity NPC269615
0.6949 Remote Similarity NPC473866
0.6949 Remote Similarity NPC474267
0.6949 Remote Similarity NPC122239
0.6897 Remote Similarity NPC474577
0.6897 Remote Similarity NPC121034
0.6889 Remote Similarity NPC250734
0.6885 Remote Similarity NPC55068
0.6875 Remote Similarity NPC306850
0.6863 Remote Similarity NPC145755
0.6863 Remote Similarity NPC267514
0.6852 Remote Similarity NPC473487
0.6852 Remote Similarity NPC20934
0.6852 Remote Similarity NPC288381
0.6842 Remote Similarity NPC329686
0.6842 Remote Similarity NPC227135
0.6833 Remote Similarity NPC327112
0.68 Remote Similarity NPC31121
0.6786 Remote Similarity NPC475723
0.678 Remote Similarity NPC469373
0.678 Remote Similarity NPC226848
0.6727 Remote Similarity NPC244038
0.6724 Remote Similarity NPC324224
0.6724 Remote Similarity NPC55412
0.6724 Remote Similarity NPC249645
0.6724 Remote Similarity NPC472808
0.6721 Remote Similarity NPC477829
0.6667 Remote Similarity NPC136164
0.6667 Remote Similarity NPC300121
0.6667 Remote Similarity NPC308844
0.6667 Remote Similarity NPC255863
0.6667 Remote Similarity NPC329424
0.6667 Remote Similarity NPC189677
0.6667 Remote Similarity NPC245947
0.6667 Remote Similarity NPC40434
0.6667 Remote Similarity NPC475931
0.6667 Remote Similarity NPC34873
0.6607 Remote Similarity NPC106531
0.6596 Remote Similarity NPC79544
0.6557 Remote Similarity NPC130807
0.6557 Remote Similarity NPC471081
0.6552 Remote Similarity NPC232247
0.6552 Remote Similarity NPC251666
0.6552 Remote Similarity NPC474913
0.6538 Remote Similarity NPC474413
0.6538 Remote Similarity NPC473539
0.6522 Remote Similarity NPC81989
0.6522 Remote Similarity NPC62779
0.6508 Remote Similarity NPC300593

  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 NPC85079 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
0.7059 Intermediate Similarity NPD4265 Approved
0.6885 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6833 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6724 Remote Similarity NPD4219 Approved
0.6271 Remote Similarity NPD4627 Clinical (unspecified phase)
0.623 Remote Similarity NPD585 Clinical (unspecified phase)
0.619 Remote Similarity NPD368 Approved
0.6176 Remote Similarity NPD3212 Clinical (unspecified phase)
0.6071 Remote Similarity NPD4220 Pre-registration
0.6 Remote Similarity NPD342 Phase 1
0.6 Remote Similarity NPD3197 Phase 1
0.597 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5844 Remote Similarity NPD5332 Approved
0.5844 Remote Similarity NPD5331 Approved
0.5833 Remote Similarity NPD8264 Approved
0.5818 Remote Similarity NPD39 Approved
0.5775 Remote Similarity NPD4732 Discontinued
0.5692 Remote Similarity NPD4194 Approved
0.5692 Remote Similarity NPD4193 Approved
0.5692 Remote Similarity NPD4191 Approved
0.5692 Remote Similarity NPD4192 Approved
0.569 Remote Similarity NPD2268 Discontinued
0.5667 Remote Similarity NPD3172 Approved
0.56 Remote Similarity NPD5784 Clinical (unspecified phase)
0.56 Remote Similarity NPD4271 Approved
0.56 Remote Similarity NPD7322 Clinical (unspecified phase)
0.56 Remote Similarity NPD4268 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