Natural Product: NPC72699

Natural Product IDNPC72699
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Oplopandiol
IUPAC Name (Z,3S,8S)-heptadec-9-en-4,6-diyne-3,8-diol
Synonyms Oplopandiol
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL463219
PubChem CID 6474833
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

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey CGMZKZLQZWZKJO-RCQSYPNMSA-N
Standard InCHI InChI=1S/C17H26O2/c1-3-5-6-7-8-9-10-14-17(19)15-12-11-13-16(18)4-2/h10,14,16-19H,3-9H2,1-2H3/b14-10-/t16-,17-/m0/s1
SMILES CCCCCCC/C=C[C@@H](C#CC#C[C@H](CC)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   262.19 Volume:   306.986
?
Van der Waals volume.
Dense:   0.854 LogP:   3.938
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.176
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.61
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   3.0
TPSA:   40.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.401 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.983 Fsp3:   0.647
MCE-18:   2.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.116 Fluc inhibitor:   0.002
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.018
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.795 Promiscuous compounds:   0.082

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.925 MDCK Permeability:   -4.713
Pgp-inhibitor:   0.028 Pgp-substrate:   0.0
PAMPA:   0.994
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.0
20% Bioavailability (F20%):   0.0 30% Bioavailability (F30%):   0.0
50% Bioavailability (F50%):   0.963

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.0
Plasma Protein Binding (PPB):   98.406% Volume Distribution (VD):   -0.035
Fu: 0.991%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.0
OATP1B3 inhibitor:   0.0 BCRP inhibitor:   1.0
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.984
CYP2C19-inhibitor:   0.033 CYP2C19-substrate:   0.079
CYP2C9-inhibitor:   0.886 CYP2C9-substrate:   0.2
CYP2D6-inhibitor:   0.487 CYP2D6-substrate:   0.892
CYP3A4-inhibitor:   0.004 CYP3A4-substrate:   0.992
CYP2B6-substrate:   0.001 CYP2C8-inhibitor:   0.999
HLM stability:   0.317
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  5.178 Half-life (T1/2):  1.514

ADMET: Toxicity

hERG Blockers:  0.085 hERG Blockers (10um):  0.818
Human Hepatotoxicity (H-HT):  0.244 Drug-induced Liver Injury (DILI):  0.66
AMES Toxicity:  0.297 Rat Oral Acute Toxicity:  0.635
Maximum Recommended Daily Dose:  0.744 Skin Sensitization:  0.971
Carcinogencity:  0.354 Eye Corrosion:  0.999
Eye Irritation:  0.998 Respiratory Toxicity:  1.0
Drug-induced Neurotoxicity:  0.141 Ototoxicity:  0.344
Hematotoxicity:  0.005 Drug-induced Nephrotoxicity:  0.026
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.104
A549 Cytotoxicity:  0.121 Hek293 Cytotoxicity:  0.683
BCF:   1.564
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   4.513
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.793
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.122
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[20218656]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota stems n.a. n.a. PMID[20387902]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota Tubers n.a. n.a. PMID[23356207]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36838931]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37480748]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[9392889]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25663 Piscidia piscipula Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24374 Brunsvigia orientalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23922 Helichrysum oxyphyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25131 Parmelia weberi Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23679 Streptomyces roseiscleroticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23679 Streptomyces roseiscleroticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25663 Piscidia piscipula Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24374 Brunsvigia orientalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23922 Helichrysum oxyphyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25695 Oplopanax horridus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25131 Parmelia weberi Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
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 Organism Name 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

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1785 Individual protein Serotonin 7 (5-HT7) receptor Homo sapiens Inhibition = 5.0 % PMID[16643021]
NPT99 Individual protein Peroxisome proliferator-activated receptor gamma Homo sapiens FC = 2.5 n.a. PMID[32129622]

In vitro 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[20387902]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 2990.0 nM PMID[20387902]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 2720.0 nM PMID[20387902]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 6.25 ug.mL-1 PMID[9392889]
NPT20 Organism Candida albicans Candida albicans MIC = 12.5 ug.mL-1 PMID[9392889]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 61.5 ug.mL-1 PMID[20218656]
NPT19 Organism Escherichia coli Escherichia coli MIC = 6.25 ug.mL-1 PMID[9392889]
NPT19 Organism Escherichia coli Escherichia coli MIC > 50.0 ug.mL-1 PMID[9392889]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 50.0 ug.mL-1 PMID[9392889]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 6.25 ug.mL-1 PMID[9392889]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC72699 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8438 Intermediate Similarity NPC153538
0.7941 Intermediate Similarity NPC484320
0.7941 Intermediate Similarity NPC168510
0.7812 Intermediate Similarity NPC91226
0.7812 Intermediate Similarity NPC243546
0.7812 Intermediate Similarity NPC31194
0.7812 Intermediate Similarity NPC248884
0.675 Remote Similarity NPC29697
0.6579 Remote Similarity NPC85079
0.6579 Remote Similarity NPC151782
0.6471 Remote Similarity NPC124183
0.6471 Remote Similarity NPC482802
0.6389 Remote Similarity NPC93639
0.625 Remote Similarity NPC249670
0.6061 Remote Similarity NPC474642
0.6061 Remote Similarity NPC473913
0.6053 Remote Similarity NPC482801
0.5897 Remote Similarity NPC142092
0.5814 Remote Similarity NPC193975
0.5714 Remote Similarity NPC243813
0.561 Remote Similarity NPC470966
0.5476 Remote Similarity NPC477661
0.5476 Remote Similarity NPC603233
0.5476 Remote Similarity NPC607245
0.5385 Remote Similarity NPC55063
0.5385 Remote Similarity NPC19834
0.5385 Remote Similarity NPC481858
0.5385 Remote Similarity NPC166942
0.5366 Remote Similarity NPC35141
0.5349 Remote Similarity NPC66460
0.5349 Remote Similarity NPC325929
0.5349 Remote Similarity NPC470970
0.5349 Remote Similarity NPC271282
0.5312 Remote Similarity NPC125122
0.5312 Remote Similarity NPC471276
0.5312 Remote Similarity NPC471280
0.5312 Remote Similarity NPC471281
0.5263 Remote Similarity NPC484322
0.5263 Remote Similarity NPC473865
0.5227 Remote Similarity NPC610667
0.5152 Remote Similarity NPC170776
0.5152 Remote Similarity NPC9273
0.5152 Remote Similarity NPC165447
0.5152 Remote Similarity NPC471959
0.5152 Remote Similarity NPC199286
0.5152 Remote Similarity NPC489046
0.5152 Remote Similarity NPC76198
0.5152 Remote Similarity NPC610719
0.5111 Remote Similarity NPC470969
0.5111 Remote Similarity NPC212730

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC72699 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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