Natural Product: NPC305267

Natural Product IDNPC305267
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Dianversicoside F
IUPAC Name 8a-O-[(2S,3R,4S,5S,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]-3,4,5-trihydroxyoxan-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 F
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL553463
PubChem CID 42640291
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 VBBKYJHEVPBGBQ-MSXWTUGRSA-N
Standard InCHI InChI=1S/C54H86O26/c1-49(2)13-14-54(48(72)80-45-41(70)37(66)34(63)26(77-45)20-73-46-42(38(67)33(62)25(19-57)76-46)78-43-39(68)35(64)31(60)23(17-55)74-43)22(15-49)21-7-8-27-50(3)11-10-29(58)53(6,28(50)9-12-51(27,4)52(21,5)16-30(54)59)47(71)79-44-40(69)36(65)32(61)24(18-56)75-44/h7,22-46,55-70H,8-20H2,1-6H3/t22-,23+,24+,25+,26+,27+,28+,29-,30+,31+,32+,33+,34+,35-,36-,37-,38-,39+,40+,41+,42+,43-,44-,45-,46+,50+,51+,52+,53-,54+/m0/s1
SMILES OC[C@H]1O[C@@H](OC[C@H]2O[C@@H](OC(=O)[C@@]34CCC(C[C@H]4C4=CC[C@H]5[C@@]([C@@]4(C[C@H]3O)C)(C)CC[C@@H]3[C@]5(C)CC[C@@H]([C@@]3(C)C(=O)O[C@@H]3O[C@H](CO)[C@H]([C@@H]([C@H]3O)O)O)O)(C)C)[C@@H]([C@H]([C@@H]2O)O)O)[C@@H]([C@H]([C@@H]1O)O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1150.54 Volume:   1086.168
?
Van der Waals volume.
Dense:   1.059 LogP:   -0.819
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.381
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.506
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   52.0
TPSA:   431.66
?
Topological Polar Surface Area.
H-Bond Acceptor:   26.0
H-Bond Donor:   16.0 Rings:   9.0
Heavy Atoms:   26.0

MedChem Properties

QED Drug-Likeness Score:   0.065 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.006 Fsp3:   0.926
MCE-18:   202.154
?
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:   0.67 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.015
?
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:   0.224 Promiscuous compounds:   0.162

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.853 MDCK Permeability:   -5.023
Pgp-inhibitor:   0.0 Pgp-substrate:   0.179
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):   0.999
20% Bioavailability (F20%):   0.873 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.797 MRP1:   0.003
Plasma Protein Binding (PPB):   64.037% Volume Distribution (VD):   -0.256
Fu: 19.556%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.003
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:   0.034
HLM stability:   0.0
?
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):  -0.731 Half-life (T1/2):  5.065

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.801 Drug-induced Liver Injury (DILI):  0.984
AMES Toxicity:  0.994 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.125 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.785 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.85 RPMI-8226 Immunitoxicity:  0.271
A549 Cytotoxicity:  0.945 Hek293 Cytotoxicity:  0.196
BCF:   0.554
?
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:   3.287
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.947
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.849
?
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 = 4400.0 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 = 9700.0 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 NPC305267 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 NPC69811
0.819 Intermediate Similarity NPC25663
0.7522 Intermediate Similarity NPC476991
0.6634 Remote Similarity NPC475208
0.6535 Remote Similarity NPC1046
0.6449 Remote Similarity NPC164389
0.6442 Remote Similarity NPC480420
0.6422 Remote Similarity NPC64715
0.6373 Remote Similarity NPC29069
0.6372 Remote Similarity NPC476992
0.6296 Remote Similarity NPC488526
0.626 Remote Similarity NPC220160
0.6162 Remote Similarity NPC48249
0.6142 Remote Similarity NPC33012
0.6129 Remote Similarity NPC51564
0.6121 Remote Similarity NPC123522
0.6102 Remote Similarity NPC283417
0.6102 Remote Similarity NPC200049
0.6091 Remote Similarity NPC63159
0.6063 Remote Similarity NPC8524
0.6053 Remote Similarity NPC104137
0.6053 Remote Similarity NPC26626
0.6 Remote Similarity NPC48499
0.5984 Remote Similarity NPC475514
0.5962 Remote Similarity NPC238935
0.595 Remote Similarity NPC21691
0.5918 Remote Similarity NPC167383
0.5913 Remote Similarity NPC207738
0.5872 Remote Similarity NPC469946
0.5868 Remote Similarity NPC4749
0.5862 Remote Similarity NPC815
0.5856 Remote Similarity NPC473459
0.5854 Remote Similarity NPC470876
0.5804 Remote Similarity NPC105800
0.58 Remote Similarity NPC237503
0.578 Remote Similarity NPC295371
0.5726 Remote Similarity NPC75287
0.5691 Remote Similarity NPC473386
0.5625 Remote Similarity NPC104071
0.561 Remote Similarity NPC85154
0.5593 Remote Similarity NPC11242
0.5583 Remote Similarity NPC79643
0.5575 Remote Similarity NPC102439
0.5575 Remote Similarity NPC232237
0.5574 Remote Similarity NPC480423
0.5536 Remote Similarity NPC112352
0.552 Remote Similarity NPC473452
0.552 Remote Similarity NPC13998
0.552 Remote Similarity NPC286457
0.5504 Remote Similarity NPC482010
0.55 Remote Similarity NPC610204
0.5492 Remote Similarity NPC135904
0.5492 Remote Similarity NPC123199
0.5487 Remote Similarity NPC309714
0.5481 Remote Similarity NPC489208
0.5478 Remote Similarity NPC222580
0.5478 Remote Similarity NPC123796
0.5478 Remote Similarity NPC488517
0.547 Remote Similarity NPC481079
0.5469 Remote Similarity NPC309223
0.5447 Remote Similarity NPC191827
0.5431 Remote Similarity NPC471435
0.5431 Remote Similarity NPC471434
0.542 Remote Similarity NPC102505
0.542 Remote Similarity NPC488514
0.5417 Remote Similarity NPC185466
0.5403 Remote Similarity NPC471577
0.5366 Remote Similarity NPC603137
0.5349 Remote Similarity NPC302543
0.5349 Remote Similarity NPC144644
0.5349 Remote Similarity NPC170407
0.5345 Remote Similarity NPC297263
0.5323 Remote Similarity NPC470218
0.5319 Remote Similarity NPC488519
0.5312 Remote Similarity NPC293330
0.5312 Remote Similarity NPC65105
0.5312 Remote Similarity NPC43550
0.5304 Remote Similarity NPC148603
0.5304 Remote Similarity NPC480475
0.5268 Remote Similarity NPC150400
0.5267 Remote Similarity NPC142151
0.5263 Remote Similarity NPC489209
0.5252 Remote Similarity NPC484831
0.5252 Remote Similarity NPC484830
0.525 Remote Similarity NPC31838
0.5246 Remote Similarity NPC60557
0.5246 Remote Similarity NPC76972
0.5246 Remote Similarity NPC469782
0.5246 Remote Similarity NPC67857
0.5246 Remote Similarity NPC204414
0.5238 Remote Similarity NPC604133
0.5234 Remote Similarity NPC41061
0.5234 Remote Similarity NPC227551
0.5231 Remote Similarity NPC37860
0.5229 Remote Similarity NPC214484
0.5227 Remote Similarity NPC250247
0.5221 Remote Similarity NPC470512
0.5221 Remote Similarity NPC39211
0.5205 Remote Similarity NPC23020
0.5191 Remote Similarity NPC70809
0.5188 Remote Similarity NPC68767
0.5179 Remote Similarity NPC475516
0.5175 Remote Similarity NPC473343
0.5172 Remote Similarity NPC251768
0.5172 Remote Similarity NPC485563
0.5169 Remote Similarity NPC302887
0.5167 Remote Similarity NPC160452
0.5154 Remote Similarity NPC135849
0.5154 Remote Similarity NPC305981
0.5152 Remote Similarity NPC267694
0.5149 Remote Similarity NPC153673
0.5149 Remote Similarity NPC51099
0.5143 Remote Similarity NPC306746
0.5133 Remote Similarity NPC473373
0.513 Remote Similarity NPC192791
0.513 Remote Similarity NPC223301
0.513 Remote Similarity NPC171544
0.5126 Remote Similarity NPC104372
0.5124 Remote Similarity NPC481078
0.5122 Remote Similarity NPC610461
0.5116 Remote Similarity NPC471580
0.5116 Remote Similarity NPC258617
0.5115 Remote Similarity NPC261506
0.5115 Remote Similarity NPC298034
0.5115 Remote Similarity NPC71065
0.5115 Remote Similarity NPC4328
0.5105 Remote Similarity NPC233223
0.5105 Remote Similarity NPC183816
0.5105 Remote Similarity NPC43589
0.5098 Remote Similarity NPC191763
0.5086 Remote Similarity NPC30289
0.5085 Remote Similarity NPC470513
0.5083 Remote Similarity NPC301449
0.5083 Remote Similarity NPC601290
0.5083 Remote Similarity NPC606145
0.5081 Remote Similarity NPC151543
0.5079 Remote Similarity NPC475160
0.5079 Remote Similarity NPC100639
0.5079 Remote Similarity NPC473714
0.5075 Remote Similarity NPC293031
0.5043 Remote Similarity NPC173859
0.5041 Remote Similarity NPC295823
0.5041 Remote Similarity NPC174720
0.5041 Remote Similarity NPC241909
0.5041 Remote Similarity NPC213952
0.5041 Remote Similarity NPC475467
0.5037 Remote Similarity NPC110385
0.5036 Remote Similarity NPC275225
0.5036 Remote Similarity NPC480421
0.5035 Remote Similarity NPC484829

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC305267 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