Structure

Physi-Chem Properties

Molecular Weight:  310.21
Volume:  344.499
LogP:  3.906
LogD:  3.104
LogS:  -3.492
# Rotatable Bonds:  10
TPSA:  69.92
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.425
Synthetic Accessibility Score:  4.421
Fsp3:  0.778
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.364
MDCK Permeability:  2.8585905965883285e-05
Pgp-inhibitor:  0.007
Pgp-substrate:  0.777
Human Intestinal Absorption (HIA):  0.068
20% Bioavailability (F20%):  0.014
30% Bioavailability (F30%):  0.503

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.148
Plasma Protein Binding (PPB):  99.5725326538086%
Volume Distribution (VD):  1.501
Pgp-substrate:  2.15258526802063%

ADMET: Metabolism

CYP1A2-inhibitor:  0.115
CYP1A2-substrate:  0.305
CYP2C19-inhibitor:  0.711
CYP2C19-substrate:  0.629
CYP2C9-inhibitor:  0.725
CYP2C9-substrate:  0.956
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.088
CYP3A4-inhibitor:  0.49
CYP3A4-substrate:  0.069

ADMET: Excretion

Clearance (CL):  8.693
Half-life (T1/2):  0.441

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.438
Drug-inuced Liver Injury (DILI):  0.959
AMES Toxicity:  0.896
Rat Oral Acute Toxicity:  0.986
Maximum Recommended Daily Dose:  0.998
Skin Sensitization:  0.937
Carcinogencity:  0.051
Eye Corrosion:  0.78
Eye Irritation:  0.92
Respiratory Toxicity:  0.977

Download Data

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

  Natural Product: NPC62014

Natural Product ID:  NPC62014
Common Name*:   Oploxyne B
IUPAC Name:   (3S,8R,9R,10R)-10-methoxyheptadeca-4,6-diyne-3,8,9-triol
Synonyms:   Oploxyne B
Standard InCHIKey:  FVLOVPUOMLOXJT-BSDSXHPESA-N
Standard InCHI:  InChI=1S/C18H30O4/c1-4-6-7-8-9-14-17(22-3)18(21)16(20)13-11-10-12-15(19)5-2/h15-21H,4-9,14H2,1-3H3/t15-,16+,17+,18+/m0/s1
SMILES:  CCCCCCC[C@H]([C@@H]([C@@H](C#CC#C[C@H](CC)O)O)O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1098422
PubChem CID:   46832813
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
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[469703]

☑ 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 NPC62014 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 NPC8597
0.82 Intermediate Similarity NPC289979
0.7907 Intermediate Similarity NPC471282
0.7727 Intermediate Similarity NPC152008
0.7674 Intermediate Similarity NPC197039
0.7619 Intermediate Similarity NPC474914
0.7619 Intermediate Similarity NPC474392
0.7407 Intermediate Similarity NPC474577
0.7381 Intermediate Similarity NPC97967
0.7317 Intermediate Similarity NPC319034
0.7317 Intermediate Similarity NPC72324
0.7317 Intermediate Similarity NPC193062
0.7317 Intermediate Similarity NPC66124
0.7317 Intermediate Similarity NPC1748
0.7292 Intermediate Similarity NPC201948
0.7255 Intermediate Similarity NPC100096
0.717 Intermediate Similarity NPC469937
0.717 Intermediate Similarity NPC53463
0.717 Intermediate Similarity NPC23155
0.717 Intermediate Similarity NPC320588
0.7083 Intermediate Similarity NPC215358
0.7073 Intermediate Similarity NPC122962
0.7073 Intermediate Similarity NPC267243
0.6939 Remote Similarity NPC473914
0.6909 Remote Similarity NPC148424
0.6905 Remote Similarity NPC291158
0.6905 Remote Similarity NPC205141
0.6905 Remote Similarity NPC12231
0.6905 Remote Similarity NPC272998
0.6905 Remote Similarity NPC185538
0.6905 Remote Similarity NPC152759
0.6905 Remote Similarity NPC181516
0.6905 Remote Similarity NPC139131
0.6863 Remote Similarity NPC304162
0.6829 Remote Similarity NPC112242
0.6829 Remote Similarity NPC225783
0.6829 Remote Similarity NPC24506
0.6829 Remote Similarity NPC163556
0.6829 Remote Similarity NPC236797
0.6829 Remote Similarity NPC147096
0.6829 Remote Similarity NPC185041
0.6792 Remote Similarity NPC295765
0.6786 Remote Similarity NPC322148
0.6667 Remote Similarity NPC475560
0.6667 Remote Similarity NPC126915
0.6667 Remote Similarity NPC74352
0.6596 Remote Similarity NPC266553
0.6591 Remote Similarity NPC325034
0.6591 Remote Similarity NPC293908
0.6591 Remote Similarity NPC192065
0.6591 Remote Similarity NPC66052
0.6591 Remote Similarity NPC86412
0.6585 Remote Similarity NPC110884
0.6552 Remote Similarity NPC174485
0.6552 Remote Similarity NPC470363
0.6538 Remote Similarity NPC82512
0.6458 Remote Similarity NPC474361
0.6441 Remote Similarity NPC477757
0.6441 Remote Similarity NPC477762
0.6441 Remote Similarity NPC477753
0.6441 Remote Similarity NPC477763
0.6441 Remote Similarity NPC477755
0.6441 Remote Similarity NPC477750
0.64 Remote Similarity NPC473539
0.64 Remote Similarity NPC207656
0.64 Remote Similarity NPC469781
0.64 Remote Similarity NPC107091
0.64 Remote Similarity NPC474413
0.6364 Remote Similarity NPC139569
0.6346 Remote Similarity NPC106872
0.6341 Remote Similarity NPC223195
0.6341 Remote Similarity NPC279895
0.6341 Remote Similarity NPC159845
0.6296 Remote Similarity NPC233726
0.6296 Remote Similarity NPC23134
0.6296 Remote Similarity NPC124963
0.6279 Remote Similarity NPC182541
0.6279 Remote Similarity NPC127074
0.6279 Remote Similarity NPC149070
0.6279 Remote Similarity NPC197207
0.6279 Remote Similarity NPC187058
0.6271 Remote Similarity NPC328786
0.6271 Remote Similarity NPC474627
0.6271 Remote Similarity NPC201338
0.625 Remote Similarity NPC82315
0.625 Remote Similarity NPC49059
0.625 Remote Similarity NPC256209
0.623 Remote Similarity NPC277570
0.6226 Remote Similarity NPC26253
0.6207 Remote Similarity NPC472025
0.62 Remote Similarity NPC29721
0.62 Remote Similarity NPC70756
0.62 Remote Similarity NPC320240
0.6154 Remote Similarity NPC230789
0.6154 Remote Similarity NPC252918
0.6154 Remote Similarity NPC324004
0.6154 Remote Similarity NPC321087
0.6154 Remote Similarity NPC277475
0.6154 Remote Similarity NPC328497
0.6129 Remote Similarity NPC476702
0.6111 Remote Similarity NPC55678
0.6111 Remote Similarity NPC90904
0.6078 Remote Similarity NPC240994
0.6071 Remote Similarity NPC477724
0.6071 Remote Similarity NPC187361
0.6071 Remote Similarity NPC26102
0.6066 Remote Similarity NPC17455
0.6066 Remote Similarity NPC172622
0.6042 Remote Similarity NPC221022
0.6038 Remote Similarity NPC131770
0.6038 Remote Similarity NPC200618
0.6038 Remote Similarity NPC14144
0.6034 Remote Similarity NPC8979
0.6032 Remote Similarity NPC190418
0.6032 Remote Similarity NPC471761
0.6032 Remote Similarity NPC471760
0.6 Remote Similarity NPC227267
0.6 Remote Similarity NPC474120
0.6 Remote Similarity NPC326533
0.6 Remote Similarity NPC144829
0.6 Remote Similarity NPC474089
0.6 Remote Similarity NPC29234
0.5968 Remote Similarity NPC29697
0.5965 Remote Similarity NPC303727
0.5965 Remote Similarity NPC327257
0.5962 Remote Similarity NPC12438
0.5962 Remote Similarity NPC73906
0.5962 Remote Similarity NPC199857
0.5962 Remote Similarity NPC92246
0.5962 Remote Similarity NPC255377
0.5962 Remote Similarity NPC165846
0.5962 Remote Similarity NPC176017
0.5962 Remote Similarity NPC285364
0.5962 Remote Similarity NPC69445
0.5962 Remote Similarity NPC21209
0.5962 Remote Similarity NPC30195
0.5962 Remote Similarity NPC289758
0.5957 Remote Similarity NPC177022
0.5952 Remote Similarity NPC33415
0.5952 Remote Similarity NPC301586
0.5952 Remote Similarity NPC238135
0.5938 Remote Similarity NPC477752
0.5938 Remote Similarity NPC477756
0.5938 Remote Similarity NPC477764
0.5938 Remote Similarity NPC477751
0.5932 Remote Similarity NPC470970
0.5932 Remote Similarity NPC52012
0.5926 Remote Similarity NPC42503
0.5926 Remote Similarity NPC475153
0.5926 Remote Similarity NPC282143
0.5926 Remote Similarity NPC299781
0.5926 Remote Similarity NPC474445
0.5926 Remote Similarity NPC157193
0.5918 Remote Similarity NPC99573
0.5918 Remote Similarity NPC227707
0.5918 Remote Similarity NPC111882
0.5918 Remote Similarity NPC102981
0.5918 Remote Similarity NPC88278
0.5909 Remote Similarity NPC272426
0.5902 Remote Similarity NPC472026
0.5893 Remote Similarity NPC123814
0.5882 Remote Similarity NPC19305
0.5882 Remote Similarity NPC255837
0.5882 Remote Similarity NPC76051
0.5862 Remote Similarity NPC477725
0.5862 Remote Similarity NPC477726
0.5854 Remote Similarity NPC560
0.5849 Remote Similarity NPC88638
0.5846 Remote Similarity NPC206601
0.5846 Remote Similarity NPC148192
0.5846 Remote Similarity NPC477758
0.5846 Remote Similarity NPC104537
0.5846 Remote Similarity NPC469925
0.5846 Remote Similarity NPC127091
0.5846 Remote Similarity NPC330426
0.5846 Remote Similarity NPC271921
0.5846 Remote Similarity NPC22101
0.5846 Remote Similarity NPC477761
0.5846 Remote Similarity NPC179823
0.5846 Remote Similarity NPC477760
0.5846 Remote Similarity NPC477754
0.5846 Remote Similarity NPC477759
0.5806 Remote Similarity NPC271282
0.5806 Remote Similarity NPC66460
0.5806 Remote Similarity NPC325929
0.5806 Remote Similarity NPC145627
0.58 Remote Similarity NPC473625
0.58 Remote Similarity NPC103286
0.58 Remote Similarity NPC163746
0.5789 Remote Similarity NPC130683
0.5789 Remote Similarity NPC165198
0.5789 Remote Similarity NPC246558
0.5789 Remote Similarity NPC67660
0.5789 Remote Similarity NPC107914
0.5789 Remote Similarity NPC89145
0.5789 Remote Similarity NPC323361
0.5789 Remote Similarity NPC145112
0.5789 Remote Similarity NPC270041
0.5789 Remote Similarity NPC157514
0.5789 Remote Similarity NPC58629

  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 NPC62014 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
0.7727 Intermediate Similarity NPD7536 Approved
0.717 Intermediate Similarity NPD3730 Approved
0.717 Intermediate Similarity NPD3728 Approved
0.6905 Remote Similarity NPD5383 Approved
0.6905 Remote Similarity NPD2272 Approved
0.6607 Remote Similarity NPD2267 Suspended
0.6591 Remote Similarity NPD9052 Approved
0.6591 Remote Similarity NPD9053 Approved
0.6591 Remote Similarity NPD9051 Approved
0.64 Remote Similarity NPD9218 Clinical (unspecified phase)
0.64 Remote Similarity NPD9219 Approved
0.6327 Remote Similarity NPD8958 Phase 2
0.6327 Remote Similarity NPD8957 Approved
0.6279 Remote Similarity NPD8814 Phase 3
0.62 Remote Similarity NPD9006 Approved
0.6038 Remote Similarity NPD6125 Clinical (unspecified phase)
0.6 Remote Similarity NPD905 Approved
0.6 Remote Similarity NPD904 Phase 3
0.5962 Remote Similarity NPD8993 Phase 1
0.5962 Remote Similarity NPD8998 Phase 2
0.5962 Remote Similarity NPD8999 Phase 3
0.5962 Remote Similarity NPD8997 Approved
0.5962 Remote Similarity NPD8994 Approved
0.5962 Remote Similarity NPD9000 Phase 3
0.5952 Remote Similarity NPD8549 Clinical (unspecified phase)
0.5918 Remote Similarity NPD8996 Phase 3
0.5918 Remote Similarity NPD8995 Clinical (unspecified phase)
0.5909 Remote Similarity NPD907 Approved
0.5909 Remote Similarity NPD1461 Approved
0.5909 Remote Similarity NPD908 Approved
0.5893 Remote Similarity NPD2269 Approved
0.5893 Remote Similarity NPD3215 Phase 1
0.5833 Remote Similarity NPD8977 Phase 3
0.5833 Remote Similarity NPD8976 Approved
0.5789 Remote Similarity NPD891 Phase 3
0.5789 Remote Similarity NPD895 Approved
0.5789 Remote Similarity NPD894 Approved
0.5789 Remote Similarity NPD892 Phase 3
0.5789 Remote Similarity NPD890 Clinical (unspecified phase)
0.5789 Remote Similarity NPD893 Approved
0.5789 Remote Similarity NPD889 Approved
0.5789 Remote Similarity NPD887 Approved
0.5789 Remote Similarity NPD888 Phase 3
0.5741 Remote Similarity NPD8966 Approved
0.5741 Remote Similarity NPD8965 Approved
0.5741 Remote Similarity NPD9139 Approved
0.569 Remote Similarity NPD3729 Clinical (unspecified phase)
0.5686 Remote Similarity NPD1462 Approved
0.5686 Remote Similarity NPD8788 Approved
0.5625 Remote Similarity NPD371 Approved
0.56 Remote Similarity NPD1460 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