Natural Product: NPC69811

Natural Product IDNPC69811
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Dianversicoside E
IUPAC Name 8a-O-[(2S,3R,4S,5R,6R)-6-[[(2R,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxymethyl]-3,5-dihydroxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl] 4-O-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] (3S,4S,4aR,6aR,6bS,8R,8aR,12aS,14aR,14bR)-3,8-dihydroxy-4,6a,6b,11,11,14b-hexamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicene-4,8a-dicarboxylate
Synonyms Dianversicoside E
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL554812
PubChem CID 42640126
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene saponins

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 JGRYZOSHBHWVJX-QPLFLNKMSA-N
Standard InCHI InChI=1S/C60H96O31/c1-55(2)13-14-60(23(15-55)22-7-8-29-56(3)11-10-31(65)59(6,30(56)9-12-57(29,4)58(22,5)16-32(60)66)53(80)90-50-44(78)40(74)35(69)26(19-63)85-50)54(81)91-51-45(79)46(88-48-42(76)38(72)33(67)24(17-61)83-48)37(71)28(87-51)21-82-52-47(41(75)36(70)27(20-64)86-52)89-49-43(77)39(73)34(68)25(18-62)84-49/h7,23-52,61-79H,8-21H2,1-6H3/t23-,24+,25+,26+,27+,28+,29+,30+,31-,32+,33+,34+,35+,36+,37+,38-,39-,40-,41-,42+,43+,44+,45+,46-,47+,48-,49-,50-,51-,52+,56+,57+,58+,59-,60+/m0/s1
SMILES OC[C@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@@H](O[C@@H]([C@H]2O)CO[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O)O)O)OC(=O)[C@@]23CCC(C[C@H]3C3=CC[C@H]4[C@@]([C@@]3(C[C@H]2O)C)(C)CC[C@@H]2[C@]4(C)CC[C@@H]([C@@]2(C)C(=O)O[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O)O)(C)C)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1312.59 Volume:   1225.339
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Van der Waals volume.
Dense:   1.071 LogP:   -1.844
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.023
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.086
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The logarithm of aqueous solubility value.
Rotatable Bonds:   17.0 Rigid Bonds:   58.0
TPSA:   510.81
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Topological Polar Surface Area.
H-Bond Acceptor:   31.0
H-Bond Donor:   19.0 Rings:   10.0
Heavy Atoms:   31.0

MedChem Properties

QED Drug-Likeness Score:   0.054 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.457 Fsp3:   0.933
MCE-18:   224.845
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MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.669 Fluc inhibitor:   0.0
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.009
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.309 Promiscuous compounds:   0.169

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.314 MDCK Permeability:   -4.905
Pgp-inhibitor:   0.0 Pgp-substrate:   0.264
PAMPA:   1.0
?
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):   0.998
20% Bioavailability (F20%):   0.439 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.566 MRP1:   0.0
Plasma Protein Binding (PPB):   58.62% Volume Distribution (VD):   -0.292
Fu: 24.811%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.002
HLM stability:   0.004
?
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):  -1.391 Half-life (T1/2):  5.828

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.855 Drug-induced Liver Injury (DILI):  0.995
AMES Toxicity:  0.998 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.07 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.887 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.833 RPMI-8226 Immunitoxicity:  0.306
A549 Cytotoxicity:  0.981 Hek293 Cytotoxicity:  0.266
BCF:   0.507
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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:   3.224
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.806
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.727
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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
NPO27907 Dianthus versicolor Species Caryophyllaceae Eukaryota n.a. whole plant n.a. PMID[19290648]
NPO27907 Dianthus versicolor Species Caryophyllaceae Eukaryota aerial parts Changqing, Shangdong Province, China 2004-JUN PMID[19290648]
NPO27907 Dianthus versicolor Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27907 Dianthus versicolor Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27907 Dianthus versicolor Species Caryophyllaceae 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

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1855 Cell line HFL1 Homo sapiens IC50 = 3500.0 nM PMID[19290648]
NPT83 Cell line MCF7 Homo sapiens IC50 > 10000.0 nM PMID[19290648]
NPT65 Cell line HepG2 Homo sapiens IC50 > 10000.0 nM PMID[19290648]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 7400.0 nM PMID[19290648]

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 NPC69811 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
0.8958 High Similarity NPC305267
0.8214 Intermediate Similarity NPC476991
0.7434 Intermediate Similarity NPC25663
0.7207 Intermediate Similarity NPC476992
0.6748 Remote Similarity NPC51564
0.6522 Remote Similarity NPC75287
0.648 Remote Similarity NPC220160
0.6396 Remote Similarity NPC473459
0.6262 Remote Similarity NPC475208
0.6231 Remote Similarity NPC33012
0.621 Remote Similarity NPC475514
0.6198 Remote Similarity NPC191827
0.6168 Remote Similarity NPC1046
0.6154 Remote Similarity NPC8524
0.6106 Remote Similarity NPC164389
0.6087 Remote Similarity NPC64715
0.6048 Remote Similarity NPC21691
0.5968 Remote Similarity NPC4749
0.595 Remote Similarity NPC123522
0.584 Remote Similarity NPC85154
0.5833 Remote Similarity NPC11242
0.582 Remote Similarity NPC79643
0.5814 Remote Similarity NPC302543
0.581 Remote Similarity NPC48249
0.5806 Remote Similarity NPC283417
0.5806 Remote Similarity NPC200049
0.5804 Remote Similarity NPC150400
0.5804 Remote Similarity NPC480420
0.5794 Remote Similarity NPC473386
0.575 Remote Similarity NPC104137
0.575 Remote Similarity NPC26626
0.5736 Remote Similarity NPC135849
0.5727 Remote Similarity NPC29069
0.5726 Remote Similarity NPC123199
0.5726 Remote Similarity NPC609763
0.5703 Remote Similarity NPC470876
0.569 Remote Similarity NPC488526
0.5659 Remote Similarity NPC65105
0.5659 Remote Similarity NPC43550
0.5652 Remote Similarity NPC223301
0.5652 Remote Similarity NPC171544
0.5639 Remote Similarity NPC68767
0.5636 Remote Similarity NPC238935
0.563 Remote Similarity NPC104372
0.562 Remote Similarity NPC481078
0.561 Remote Similarity NPC610204
0.5606 Remote Similarity NPC142151
0.5597 Remote Similarity NPC51099
0.5577 Remote Similarity NPC167383
0.5574 Remote Similarity NPC815
0.5573 Remote Similarity NPC144644
0.5573 Remote Similarity NPC170407
0.5565 Remote Similarity NPC469946
0.5564 Remote Similarity NPC250247
0.5546 Remote Similarity NPC471435
0.5546 Remote Similarity NPC471434
0.5538 Remote Similarity NPC293330
0.5522 Remote Similarity NPC293031
0.5512 Remote Similarity NPC471577
0.5508 Remote Similarity NPC63159
0.5504 Remote Similarity NPC13998
0.5492 Remote Similarity NPC207738
0.5489 Remote Similarity NPC482010
0.5489 Remote Similarity NPC267694
0.5481 Remote Similarity NPC153673
0.5474 Remote Similarity NPC275225
0.5472 Remote Similarity NPC237503
0.547 Remote Similarity NPC309714
0.5462 Remote Similarity NPC41061
0.5462 Remote Similarity NPC227551
0.5462 Remote Similarity NPC475504
0.5462 Remote Similarity NPC123796
0.5455 Remote Similarity NPC309223
0.5455 Remote Similarity NPC37860
0.5439 Remote Similarity NPC475516
0.5407 Remote Similarity NPC102505
0.5407 Remote Similarity NPC488514
0.5398 Remote Similarity NPC48499
0.5385 Remote Similarity NPC473452
0.5385 Remote Similarity NPC286457
0.5379 Remote Similarity NPC305981
0.5368 Remote Similarity NPC110385
0.5357 Remote Similarity NPC489208
0.5354 Remote Similarity NPC603137
0.5338 Remote Similarity NPC261506
0.5338 Remote Similarity NPC298034
0.5338 Remote Similarity NPC71065
0.5338 Remote Similarity NPC4328
0.5302 Remote Similarity NPC23020
0.528 Remote Similarity NPC185466
0.5255 Remote Similarity NPC489209
0.5254 Remote Similarity NPC112352
0.525 Remote Similarity NPC105800
0.5238 Remote Similarity NPC610461
0.5231 Remote Similarity NPC481080
0.5227 Remote Similarity NPC471580
0.5214 Remote Similarity NPC295371
0.5207 Remote Similarity NPC222580
0.5191 Remote Similarity NPC476068
0.5191 Remote Similarity NPC237191
0.5185 Remote Similarity NPC70809
0.5149 Remote Similarity NPC202828
0.5149 Remote Similarity NPC119592
0.5149 Remote Similarity NPC236638
0.5149 Remote Similarity NPC294453
0.5149 Remote Similarity NPC481081
0.512 Remote Similarity NPC609281
0.5118 Remote Similarity NPC475287
0.5083 Remote Similarity NPC104071
0.5082 Remote Similarity NPC297263
0.5081 Remote Similarity NPC481079
0.5081 Remote Similarity NPC606145
0.5078 Remote Similarity NPC151543
0.5077 Remote Similarity NPC475160
0.5077 Remote Similarity NPC480423
0.5077 Remote Similarity NPC473714
0.5068 Remote Similarity NPC475584
0.5068 Remote Similarity NPC475152
0.5067 Remote Similarity NPC478559
0.5067 Remote Similarity NPC485563
0.5067 Remote Similarity NPC478560
0.5041 Remote Similarity NPC102439
0.5041 Remote Similarity NPC232237
0.5041 Remote Similarity NPC480475
0.5039 Remote Similarity NPC323341
0.5035 Remote Similarity NPC480421

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC69811 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