Natural Product: NPC191827

Natural Product IDNPC191827
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Dianversicoside G
IUPAC Name (3S,4S,4aR,6aR,6bS,8aS,12aS,14aR,14bR)-8a-[(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]oxycarbonyl-4,6a,6b,11,11,14b-hexamethyl-3-[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicene-4-carboxylic acid
Synonyms Dianversicoside G
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL558386
PubChem CID 42640292
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 NKURNVCWJJFIBK-VIYGISPWSA-N
Standard InCHI InChI=1S/C59H94O29/c1-54(2)13-15-59(16-14-56(4)23(24(59)17-54)7-8-30-55(3)11-10-32(85-47-41(72)33(64)25(63)21-79-47)58(6,52(76)77)31(55)9-12-57(30,56)5)53(78)88-50-44(75)45(86-48-42(73)38(69)34(65)26(18-60)81-48)37(68)29(84-50)22-80-51-46(40(71)36(67)28(20-62)83-51)87-49-43(74)39(70)35(66)27(19-61)82-49/h7,24-51,60-75H,8-22H2,1-6H3,(H,76,77)/t24-,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+,55+,56+,57+,58-,59-/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(CC2)C)(C)CC[C@@H]2[C@]4(C)CC[C@@H]([C@@]2(C)C(=O)O)O[C@@H]2OC[C@@H]([C@@H]([C@H]2O)O)O)(C)C)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1266.59 Volume:   1190.462
?
Van der Waals volume.
Dense:   1.064 LogP:   -1.067
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.754
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.821
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   16.0 Rigid Bonds:   58.0
TPSA:   470.35
?
Topological Polar Surface Area.
H-Bond Acceptor:   29.0
H-Bond Donor:   17.0 Rings:   10.0
Heavy Atoms:   29.0

MedChem Properties

QED Drug-Likeness Score:   0.042 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.341 Fsp3:   0.932
MCE-18:   220.368
?
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:   0.689 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.01
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.294 Promiscuous compounds:   0.15

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.059 MDCK Permeability:   -4.867
Pgp-inhibitor:   0.0 Pgp-substrate:   0.142
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):   0.978
20% Bioavailability (F20%):   0.076 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.007
Plasma Protein Binding (PPB):   62.201% Volume Distribution (VD):   -0.389
Fu: 23.266%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
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:   0.0
HLM stability:   0.002
?
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):  -1.047 Half-life (T1/2):  4.557

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.781 Drug-induced Liver Injury (DILI):  0.986
AMES Toxicity:  0.993 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.019 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.886 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.545 RPMI-8226 Immunitoxicity:  0.234
A549 Cytotoxicity:  0.948 Hek293 Cytotoxicity:  0.212
BCF:   0.48
?
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:   3.327
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.874
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.698
?
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 = 3300.0 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 = 6800.0 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 NPC191827 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
0.8165 Intermediate Similarity NPC75287
0.7455 Intermediate Similarity NPC609763
0.7282 Intermediate Similarity NPC209894
0.7016 Intermediate Similarity NPC135849
0.6777 Remote Similarity NPC123199
0.6696 Remote Similarity NPC469946
0.6695 Remote Similarity NPC481078
0.6612 Remote Similarity NPC79643
0.6538 Remote Similarity NPC250247
0.6393 Remote Similarity NPC300419
0.6387 Remote Similarity NPC301449
0.6387 Remote Similarity NPC601290
0.6379 Remote Similarity NPC473459
0.6325 Remote Similarity NPC63159
0.6316 Remote Similarity NPC295371
0.6311 Remote Similarity NPC476992
0.626 Remote Similarity NPC70809
0.625 Remote Similarity NPC481079
0.622 Remote Similarity NPC481080
0.6212 Remote Similarity NPC51564
0.6202 Remote Similarity NPC41061
0.6202 Remote Similarity NPC227551
0.6198 Remote Similarity NPC69811
0.616 Remote Similarity NPC323341
0.6154 Remote Similarity NPC293330
0.6154 Remote Similarity NPC65105
0.6154 Remote Similarity NPC43550
0.6134 Remote Similarity NPC475504
0.6134 Remote Similarity NPC297263
0.6111 Remote Similarity NPC166422
0.6107 Remote Similarity NPC202828
0.6107 Remote Similarity NPC119592
0.6107 Remote Similarity NPC236638
0.6107 Remote Similarity NPC294453
0.6107 Remote Similarity NPC305981
0.6107 Remote Similarity NPC481081
0.6087 Remote Similarity NPC150400
0.6061 Remote Similarity NPC261506
0.6061 Remote Similarity NPC298034
0.6061 Remote Similarity NPC71065
0.6061 Remote Similarity NPC4328
0.6016 Remote Similarity NPC187290
0.6 Remote Similarity NPC473645
0.597 Remote Similarity NPC478823
0.5966 Remote Similarity NPC251768
0.5965 Remote Similarity NPC48499
0.5938 Remote Similarity NPC470218
0.5932 Remote Similarity NPC112352
0.5906 Remote Similarity NPC471384
0.5887 Remote Similarity NPC31838
0.5882 Remote Similarity NPC309714
0.5862 Remote Similarity NPC475516
0.5852 Remote Similarity NPC478824
0.5833 Remote Similarity NPC159309
0.5833 Remote Similarity NPC86222
0.5798 Remote Similarity NPC192791
0.5798 Remote Similarity NPC223301
0.5798 Remote Similarity NPC171544
0.5789 Remote Similarity NPC471385
0.5748 Remote Similarity NPC475287
0.5736 Remote Similarity NPC135904
0.5704 Remote Similarity NPC476991
0.5702 Remote Similarity NPC480475
0.5674 Remote Similarity NPC478822
0.5649 Remote Similarity NPC488560
0.5645 Remote Similarity NPC104372
0.5645 Remote Similarity NPC114484
0.563 Remote Similarity NPC136768
0.5603 Remote Similarity NPC29069
0.5597 Remote Similarity NPC258617
0.5573 Remote Similarity NPC475160
0.5573 Remote Similarity NPC471550
0.5573 Remote Similarity NPC473714
0.5564 Remote Similarity NPC476068
0.5556 Remote Similarity NPC295823
0.5556 Remote Similarity NPC174720
0.5556 Remote Similarity NPC241909
0.5556 Remote Similarity NPC475467
0.554 Remote Similarity NPC478825
0.5528 Remote Similarity NPC475591
0.5528 Remote Similarity NPC236870
0.5524 Remote Similarity NPC475368
0.5517 Remote Similarity NPC90856
0.5507 Remote Similarity NPC224381
0.5504 Remote Similarity NPC60557
0.5504 Remote Similarity NPC76972
0.5504 Remote Similarity NPC469782
0.5504 Remote Similarity NPC67857
0.5504 Remote Similarity NPC204414
0.5504 Remote Similarity NPC610204
0.5496 Remote Similarity NPC219180
0.5489 Remote Similarity NPC4749
0.5484 Remote Similarity NPC222580
0.5462 Remote Similarity NPC139894
0.5448 Remote Similarity NPC57484
0.5447 Remote Similarity NPC305267
0.5433 Remote Similarity NPC480473
0.5433 Remote Similarity NPC480474
0.5423 Remote Similarity NPC33012
0.5397 Remote Similarity NPC276093
0.5391 Remote Similarity NPC609281
0.5373 Remote Similarity NPC487505
0.5372 Remote Similarity NPC473884
0.5372 Remote Similarity NPC488561
0.5372 Remote Similarity NPC157868
0.5362 Remote Similarity NPC302543
0.5354 Remote Similarity NPC324875
0.5354 Remote Similarity NPC292677
0.5352 Remote Similarity NPC8524
0.5349 Remote Similarity NPC11242
0.5338 Remote Similarity NPC283417
0.5338 Remote Similarity NPC200049
0.5338 Remote Similarity NPC475140
0.5323 Remote Similarity NPC40775
0.5315 Remote Similarity NPC167383
0.5303 Remote Similarity NPC475899
0.5299 Remote Similarity NPC54636
0.5294 Remote Similarity NPC110633
0.5289 Remote Similarity NPC473373
0.5286 Remote Similarity NPC220160
0.5285 Remote Similarity NPC242840
0.528 Remote Similarity NPC139044
0.5276 Remote Similarity NPC281148
0.5267 Remote Similarity NPC473824
0.5267 Remote Similarity NPC610461
0.5255 Remote Similarity NPC484942
0.5254 Remote Similarity NPC214484
0.5252 Remote Similarity NPC33068
0.5242 Remote Similarity NPC114304
0.5238 Remote Similarity NPC257468
0.5234 Remote Similarity NPC323359
0.5234 Remote Similarity NPC606145
0.5221 Remote Similarity NPC21691
0.5221 Remote Similarity NPC237503
0.5208 Remote Similarity NPC477464
0.5203 Remote Similarity NPC473343
0.5203 Remote Similarity NPC213674
0.5191 Remote Similarity NPC185466
0.5191 Remote Similarity NPC288205
0.5191 Remote Similarity NPC51465
0.5182 Remote Similarity NPC480418
0.5157 Remote Similarity NPC469778
0.5154 Remote Similarity NPC475486
0.5152 Remote Similarity NPC607904
0.5149 Remote Similarity NPC257211
0.5139 Remote Similarity NPC480422
0.5133 Remote Similarity NPC472268
0.5122 Remote Similarity NPC39211
0.5122 Remote Similarity NPC469772
0.5122 Remote Similarity NPC295941
0.512 Remote Similarity NPC30735
0.5118 Remote Similarity NPC481082
0.5118 Remote Similarity NPC164419
0.5115 Remote Similarity NPC606553
0.5113 Remote Similarity NPC123522
0.5111 Remote Similarity NPC100639
0.5083 Remote Similarity NPC1046
0.5082 Remote Similarity NPC235405
0.5082 Remote Similarity NPC59804
0.5079 Remote Similarity NPC10607
0.5079 Remote Similarity NPC104400
0.5079 Remote Similarity NPC10320
0.5079 Remote Similarity NPC46665
0.5078 Remote Similarity NPC64715
0.5078 Remote Similarity NPC484832
0.5077 Remote Similarity NPC488564
0.5075 Remote Similarity NPC133818
0.5074 Remote Similarity NPC25663
0.5067 Remote Similarity NPC297950
0.5066 Remote Similarity NPC45606
0.5041 Remote Similarity NPC249848
0.5041 Remote Similarity NPC127056
0.5041 Remote Similarity NPC107966
0.5039 Remote Similarity NPC37134
0.5038 Remote Similarity NPC207738
0.5037 Remote Similarity NPC251263
0.5037 Remote Similarity NPC480419
0.5037 Remote Similarity NPC603137
0.5036 Remote Similarity NPC85154

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC191827 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