Structure

Physi-Chem Properties

Molecular Weight:  278.19
Volume:  309.857
LogP:  4.436
LogD:  3.542
LogS:  -4.216
# Rotatable Bonds:  8
TPSA:  52.99
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.407
Synthetic Accessibility Score:  4.398
Fsp3:  0.765
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:  -4.407
MDCK Permeability:  3.059947266592644e-05
Pgp-inhibitor:  0.032
Pgp-substrate:  0.124
Human Intestinal Absorption (HIA):  0.018
20% Bioavailability (F20%):  0.05
30% Bioavailability (F30%):  0.94

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.256
Plasma Protein Binding (PPB):  99.71405029296875%
Volume Distribution (VD):  1.863
Pgp-substrate:  1.892569899559021%

ADMET: Metabolism

CYP1A2-inhibitor:  0.704
CYP1A2-substrate:  0.357
CYP2C19-inhibitor:  0.793
CYP2C19-substrate:  0.389
CYP2C9-inhibitor:  0.795
CYP2C9-substrate:  0.958
CYP2D6-inhibitor:  0.022
CYP2D6-substrate:  0.12
CYP3A4-inhibitor:  0.615
CYP3A4-substrate:  0.093

ADMET: Excretion

Clearance (CL):  9.658
Half-life (T1/2):  0.213

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.437
Drug-inuced Liver Injury (DILI):  0.962
AMES Toxicity:  0.825
Rat Oral Acute Toxicity:  0.993
Maximum Recommended Daily Dose:  0.998
Skin Sensitization:  0.942
Carcinogencity:  0.082
Eye Corrosion:  0.955
Eye Irritation:  0.974
Respiratory Toxicity:  0.985

Download Data

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

  Natural Product: NPC8597

Natural Product ID:  NPC8597
Common Name*:   Oploxyne A
IUPAC Name:   (1R,6S)-1-[(2R,3S)-3-heptyloxiran-2-yl]octa-2,4-diyne-1,6-diol
Synonyms:  
Standard InCHIKey:  SNQQXKPWASLFFZ-VVLHAWIVSA-N
Standard InCHI:  InChI=1S/C17H26O3/c1-3-5-6-7-8-13-16-17(20-16)15(19)12-10-9-11-14(18)4-2/h14-19H,3-8,13H2,1-2H3/t14-,15+,16-,17+/m0/s1
SMILES:  CCCCCCC[C@@H]1O[C@@H]1[C@@H](C#CC#C[C@H](CC)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1098421
PubChem CID:   46832812
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
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota stems n.a. n.a. PMID[20387902]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29334 Oplopanax elatus Species Araliaceae 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
NPT113 Cell Line RAW264.7 Mus musculus IC50 > 40000.0 nM PMID[480867]
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 1980.0 nM PMID[480867]
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 3080.0 nM PMID[480867]

☑ 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 NPC8597 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
0.9091 High Similarity NPC62014
0.8113 Intermediate Similarity NPC474577
0.7885 Intermediate Similarity NPC289979
0.7727 Intermediate Similarity NPC197039
0.7556 Intermediate Similarity NPC471282
0.7391 Intermediate Similarity NPC152008
0.7273 Intermediate Similarity NPC474914
0.7273 Intermediate Similarity NPC474392
0.7045 Intermediate Similarity NPC97967
0.7 Intermediate Similarity NPC201948
0.6977 Remote Similarity NPC1748
0.6977 Remote Similarity NPC193062
0.6977 Remote Similarity NPC319034
0.6977 Remote Similarity NPC72324
0.6977 Remote Similarity NPC66124
0.6909 Remote Similarity NPC23155
0.6909 Remote Similarity NPC469937
0.6909 Remote Similarity NPC53463
0.6909 Remote Similarity NPC320588
0.6818 Remote Similarity NPC139569
0.68 Remote Similarity NPC215358
0.6744 Remote Similarity NPC122962
0.6744 Remote Similarity NPC267243
0.6667 Remote Similarity NPC100096
0.6667 Remote Similarity NPC148424
0.6667 Remote Similarity NPC473914
0.6604 Remote Similarity NPC304162
0.6591 Remote Similarity NPC272998
0.6591 Remote Similarity NPC12231
0.6591 Remote Similarity NPC152759
0.6591 Remote Similarity NPC291158
0.6591 Remote Similarity NPC205141
0.6591 Remote Similarity NPC185538
0.6591 Remote Similarity NPC139131
0.6591 Remote Similarity NPC181516
0.6552 Remote Similarity NPC322148
0.6545 Remote Similarity NPC295765
0.6512 Remote Similarity NPC163556
0.6512 Remote Similarity NPC112242
0.6512 Remote Similarity NPC147096
0.6512 Remote Similarity NPC185041
0.6512 Remote Similarity NPC225783
0.6512 Remote Similarity NPC24506
0.6512 Remote Similarity NPC236797
0.6452 Remote Similarity NPC476702
0.6429 Remote Similarity NPC475560
0.6393 Remote Similarity NPC172622
0.6383 Remote Similarity NPC74352
0.6364 Remote Similarity NPC126915
0.6349 Remote Similarity NPC474402
0.6333 Remote Similarity NPC470363
0.6333 Remote Similarity NPC174485
0.6327 Remote Similarity NPC266553
0.6296 Remote Similarity NPC82512
0.6296 Remote Similarity NPC26253
0.6279 Remote Similarity NPC110884
0.623 Remote Similarity NPC477750
0.623 Remote Similarity NPC477763
0.623 Remote Similarity NPC477753
0.623 Remote Similarity NPC477755
0.623 Remote Similarity NPC477757
0.623 Remote Similarity NPC477762
0.6226 Remote Similarity NPC88638
0.62 Remote Similarity NPC474361
0.619 Remote Similarity NPC199937
0.6154 Remote Similarity NPC474413
0.6154 Remote Similarity NPC469781
0.6154 Remote Similarity NPC473539
0.6129 Remote Similarity NPC17455
0.6111 Remote Similarity NPC106872
0.6087 Remote Similarity NPC227267
0.6078 Remote Similarity NPC144829
0.6071 Remote Similarity NPC23134
0.6071 Remote Similarity NPC124963
0.6071 Remote Similarity NPC233726
0.6066 Remote Similarity NPC201338
0.6066 Remote Similarity NPC328786
0.6066 Remote Similarity NPC474627
0.6061 Remote Similarity NPC82315
0.6047 Remote Similarity NPC159845
0.6047 Remote Similarity NPC223195
0.6047 Remote Similarity NPC238135
0.6047 Remote Similarity NPC279895
0.6034 Remote Similarity NPC256209
0.6034 Remote Similarity NPC49059
0.6032 Remote Similarity NPC277570
0.6 Remote Similarity NPC472025
0.5962 Remote Similarity NPC320240
0.5962 Remote Similarity NPC29721
0.5962 Remote Similarity NPC70756
0.5957 Remote Similarity NPC66052
0.5957 Remote Similarity NPC86412
0.5957 Remote Similarity NPC325034
0.5957 Remote Similarity NPC192065
0.5957 Remote Similarity NPC293908
0.5926 Remote Similarity NPC252918
0.5926 Remote Similarity NPC321087
0.5926 Remote Similarity NPC328497
0.5926 Remote Similarity NPC324004
0.5926 Remote Similarity NPC230789
0.5926 Remote Similarity NPC277475
0.5909 Remote Similarity NPC161612
0.5909 Remote Similarity NPC33583
0.5902 Remote Similarity NPC476209
0.5893 Remote Similarity NPC55678
0.5893 Remote Similarity NPC90904
0.5862 Remote Similarity NPC187361
0.5862 Remote Similarity NPC26102
0.5862 Remote Similarity NPC477724
0.5849 Remote Similarity NPC107091
0.5849 Remote Similarity NPC240994
0.5849 Remote Similarity NPC207656
0.5846 Remote Similarity NPC471760
0.5846 Remote Similarity NPC471761
0.5846 Remote Similarity NPC190418
0.5833 Remote Similarity NPC8979
0.5818 Remote Similarity NPC131770
0.5818 Remote Similarity NPC14144
0.5818 Remote Similarity NPC200618
0.5814 Remote Similarity NPC272307
0.5806 Remote Similarity NPC185116
0.58 Remote Similarity NPC221022
0.5789 Remote Similarity NPC29234
0.5789 Remote Similarity NPC326533
0.5781 Remote Similarity NPC29697
0.5769 Remote Similarity NPC31121
0.5763 Remote Similarity NPC303727
0.5758 Remote Similarity NPC477752
0.5758 Remote Similarity NPC477764
0.5758 Remote Similarity NPC477751
0.5758 Remote Similarity NPC477756
0.5741 Remote Similarity NPC289758
0.5741 Remote Similarity NPC73906
0.5741 Remote Similarity NPC199857
0.5741 Remote Similarity NPC176017
0.5741 Remote Similarity NPC69445
0.5741 Remote Similarity NPC92246
0.5741 Remote Similarity NPC30195
0.5741 Remote Similarity NPC255377
0.5741 Remote Similarity NPC165846
0.5741 Remote Similarity NPC21209
0.5741 Remote Similarity NPC285364
0.5741 Remote Similarity NPC12438
0.5714 Remote Similarity NPC157193
0.5714 Remote Similarity NPC472026
0.5714 Remote Similarity NPC475412
0.5714 Remote Similarity NPC42503
0.5714 Remote Similarity NPC177022
0.5714 Remote Similarity NPC128996
0.5714 Remote Similarity NPC475153
0.5714 Remote Similarity NPC282143
0.5714 Remote Similarity NPC299781
0.5714 Remote Similarity NPC476709
0.569 Remote Similarity NPC123814
0.569 Remote Similarity NPC142092
0.5672 Remote Similarity NPC330426
0.5672 Remote Similarity NPC477760
0.5672 Remote Similarity NPC477761
0.5672 Remote Similarity NPC477754
0.5672 Remote Similarity NPC477758
0.5672 Remote Similarity NPC104537
0.5672 Remote Similarity NPC206601
0.5672 Remote Similarity NPC22101
0.5672 Remote Similarity NPC271921
0.5672 Remote Similarity NPC477759
0.5672 Remote Similarity NPC127091
0.5672 Remote Similarity NPC469925
0.5672 Remote Similarity NPC179823
0.5672 Remote Similarity NPC148192
0.5667 Remote Similarity NPC477726
0.5667 Remote Similarity NPC477725
0.566 Remote Similarity NPC76051
0.566 Remote Similarity NPC255837
0.566 Remote Similarity NPC19305
0.5652 Remote Similarity NPC182541
0.5652 Remote Similarity NPC149070
0.5652 Remote Similarity NPC127074
0.5652 Remote Similarity NPC129630
0.5652 Remote Similarity NPC197207
0.5652 Remote Similarity NPC470268
0.5652 Remote Similarity NPC187058
0.5645 Remote Similarity NPC182903
0.5634 Remote Similarity NPC471525
0.5625 Remote Similarity NPC475807
0.5625 Remote Similarity NPC223374
0.5625 Remote Similarity NPC301398
0.5625 Remote Similarity NPC271282
0.5625 Remote Similarity NPC196442
0.5625 Remote Similarity NPC325929
0.5625 Remote Similarity NPC86545
0.5625 Remote Similarity NPC66460
0.5606 Remote Similarity NPC165069
0.5606 Remote Similarity NPC238646

  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 NPC8597 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
0.7391 Intermediate Similarity NPD7536 Approved
0.6909 Remote Similarity NPD3730 Approved
0.6909 Remote Similarity NPD3728 Approved
0.6591 Remote Similarity NPD2272 Approved
0.6591 Remote Similarity NPD5383 Approved
0.64 Remote Similarity NPD8958 Phase 2
0.6379 Remote Similarity NPD2267 Suspended
0.6078 Remote Similarity NPD8957 Approved
0.5962 Remote Similarity NPD9006 Approved
0.5957 Remote Similarity NPD9052 Approved
0.5957 Remote Similarity NPD9051 Approved
0.5957 Remote Similarity NPD9053 Approved
0.5849 Remote Similarity NPD9219 Approved
0.5849 Remote Similarity NPD9218 Clinical (unspecified phase)
0.5818 Remote Similarity NPD6125 Clinical (unspecified phase)
0.5789 Remote Similarity NPD904 Phase 3
0.5789 Remote Similarity NPD905 Approved
0.5741 Remote Similarity NPD8998 Phase 2
0.5741 Remote Similarity NPD8999 Phase 3
0.5741 Remote Similarity NPD8993 Phase 1
0.5741 Remote Similarity NPD9000 Phase 3
0.5741 Remote Similarity NPD8997 Approved
0.5741 Remote Similarity NPD8994 Approved
0.5692 Remote Similarity NPD371 Approved
0.569 Remote Similarity NPD2269 Approved
0.569 Remote Similarity NPD3215 Phase 1
0.5652 Remote Similarity NPD8814 Phase 3

  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