Natural Product: NPC30279

Natural Product IDNPC30279
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Sasanquasaponin Ii
IUPAC Name (2S,3S,4S,5R,6R)-6-[[(3S,4aR,6aR,6bS,7R,8S,8aR,9S,12aS,14aR,14bR)-7,8-dihydroxy-8a-(hydroxymethyl)-4,4,6a,6b,11,11,14b-heptamethyl-9-[(E)-2-methylbut-2-enoyl]oxy-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy]-4-[(2S,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxy-3-hydroxy-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxane-2-carboxylic acid
Synonyms Sasanquasaponin II
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2087226
PubChem CID 49871629
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 KHFDIHQNZXOTAA-SYHYSKNMSA-N
Standard InCHI InChI=1S/C59H94O26/c1-11-23(2)49(76)80-32-19-54(4,5)18-26-25-12-13-30-56(8)16-15-31(55(6,7)29(56)14-17-57(30,9)58(25,10)46(72)47(73)59(26,32)22-62)81-53-45(85-51-40(70)37(67)34(64)27(20-60)78-51)42(41(71)43(83-53)48(74)75)82-52-44(38(68)35(65)28(21-61)79-52)84-50-39(69)36(66)33(63)24(3)77-50/h11-12,24,26-47,50-53,60-73H,13-22H2,1-10H3,(H,74,75)/b23-11+/t24-,26-,27+,28+,29-,30+,31-,32-,33-,34+,35-,36+,37-,38-,39+,40+,41-,42-,43-,44+,45+,46-,47+,50-,51-,52-,53+,56-,57+,58-,59+/m0/s1
SMILES C/C=C(C)/C(=O)O[C@H]1CC(C)(C)C[C@H]2C3=CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]4(C)[C@]3(C)[C@H]([C@H]([C@@]12CO)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O1)O)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](CO)O1)O)O)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1218.6 Volume:   1170.012
?
Van der Waals volume.
Dense:   1.042 LogP:   0.451
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.814
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.506
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The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   53.0
TPSA:   420.66
?
Topological Polar Surface Area.
H-Bond Acceptor:   26.0
H-Bond Donor:   15.0 Rings:   9.0
Heavy Atoms:   26.0

MedChem Properties

QED Drug-Likeness Score:   0.039 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.309 Fsp3:   0.898
MCE-18:   206.286
?
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:   0.701 Fluc inhibitor:   0.004
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
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:   0.291 Promiscuous compounds:   0.259

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.258 MDCK Permeability:   -5.153
Pgp-inhibitor:   0.0 Pgp-substrate:   0.983
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%):   0.947 30% Bioavailability (F30%):   0.997
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.71
Plasma Protein Binding (PPB):   62.363% Volume Distribution (VD):   -0.358
Fu: 21.028%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.578 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:   0.634
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):  -0.6 Half-life (T1/2):  4.092

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.402 Drug-induced Liver Injury (DILI):  0.923
AMES Toxicity:  0.92 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.011 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.579 Drug-induced Nephrotoxicity:  0.998
Genotoxicity:  0.489 RPMI-8226 Immunitoxicity:  0.241
A549 Cytotoxicity:  0.225 Hek293 Cytotoxicity:  0.078
BCF:   0.404
?
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:   3.343
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.078
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.787
?
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
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. leaf n.a. PMID[16926516]
NPO23380 Camellia japonica Species Theaceae Eukaryota flower buds n.a. n.a. PMID[22834923]
NPO23380 Camellia japonica Species Theaceae Eukaryota Roots n.a. n.a. PMID[30395460]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. PMID[32569471]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. PMID[39065796]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23380 Camellia japonica Species Theaceae 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
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 16.5 % PMID[22834923]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 48.9 % PMID[22834923]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 16.8 % PMID[22834923]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 53.9 % PMID[22834923]

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 NPC30279 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
1.0 High Similarity NPC277212
0.8727 High Similarity NPC473918
0.8727 High Similarity NPC46823
0.8584 High Similarity NPC225791
0.8509 High Similarity NPC484059
0.8509 High Similarity NPC484060
0.8482 Intermediate Similarity NPC71391
0.8407 Intermediate Similarity NPC484061
0.8407 Intermediate Similarity NPC484062
0.7522 Intermediate Similarity NPC329976
0.7479 Intermediate Similarity NPC178264
0.7395 Intermediate Similarity NPC192765
0.7339 Intermediate Similarity NPC484063
0.7339 Intermediate Similarity NPC484064
0.7273 Intermediate Similarity NPC265841
0.7193 Intermediate Similarity NPC477075
0.7193 Intermediate Similarity NPC477076
0.7167 Intermediate Similarity NPC47995
0.7155 Intermediate Similarity NPC605294
0.713 Intermediate Similarity NPC477077
0.6724 Remote Similarity NPC302887
0.6639 Remote Similarity NPC609281
0.6614 Remote Similarity NPC476779
0.6555 Remote Similarity NPC160452
0.6555 Remote Similarity NPC477078
0.6549 Remote Similarity NPC603026
0.6535 Remote Similarity NPC271610
0.6529 Remote Similarity NPC25998
0.6471 Remote Similarity NPC477079
0.6446 Remote Similarity NPC480939
0.64 Remote Similarity NPC264566
0.64 Remote Similarity NPC602995
0.6356 Remote Similarity NPC470913
0.6341 Remote Similarity NPC609119
0.626 Remote Similarity NPC478152
0.626 Remote Similarity NPC478151
0.625 Remote Similarity NPC470914
0.623 Remote Similarity NPC469947
0.623 Remote Similarity NPC480948
0.6198 Remote Similarity NPC23275
0.6172 Remote Similarity NPC181066
0.6172 Remote Similarity NPC329828
0.6107 Remote Similarity NPC484833
0.6077 Remote Similarity NPC476780
0.6063 Remote Similarity NPC478150
0.6048 Remote Similarity NPC606553
0.6031 Remote Similarity NPC312650
0.6 Remote Similarity NPC475591
0.6 Remote Similarity NPC236870
0.5954 Remote Similarity NPC488308
0.594 Remote Similarity NPC476777
0.5923 Remote Similarity NPC329923
0.5923 Remote Similarity NPC475281
0.5917 Remote Similarity NPC44716
0.5891 Remote Similarity NPC283417
0.5891 Remote Similarity NPC200049
0.5854 Remote Similarity NPC114692
0.5833 Remote Similarity NPC476774
0.5827 Remote Similarity NPC313110
0.5822 Remote Similarity NPC477474
0.582 Remote Similarity NPC131469
0.5798 Remote Similarity NPC22956
0.5778 Remote Similarity NPC302543
0.5772 Remote Similarity NPC95437
0.5758 Remote Similarity NPC470518
0.5736 Remote Similarity NPC477465
0.5735 Remote Similarity NPC476775
0.5714 Remote Similarity NPC187290
0.5704 Remote Similarity NPC329657
0.5703 Remote Similarity NPC610461
0.5702 Remote Similarity NPC605226
0.5693 Remote Similarity NPC488309
0.5685 Remote Similarity NPC477467
0.5682 Remote Similarity NPC301639
0.5682 Remote Similarity NPC478065
0.5678 Remote Similarity NPC25605
0.5672 Remote Similarity NPC262796
0.5672 Remote Similarity NPC45346
0.5659 Remote Similarity NPC478600
0.5659 Remote Similarity NPC478599
0.5646 Remote Similarity NPC477470
0.5646 Remote Similarity NPC477472
0.5635 Remote Similarity NPC187618
0.5625 Remote Similarity NPC470475
0.5588 Remote Similarity NPC475377
0.5588 Remote Similarity NPC476074
0.5556 Remote Similarity NPC606145
0.554 Remote Similarity NPC476778
0.5522 Remote Similarity NPC21691
0.5512 Remote Similarity NPC120116
0.55 Remote Similarity NPC476776
0.5489 Remote Similarity NPC470912
0.5476 Remote Similarity NPC236657
0.5474 Remote Similarity NPC110700
0.5462 Remote Similarity NPC607904
0.5462 Remote Similarity NPC610204
0.5426 Remote Similarity NPC470915
0.5424 Remote Similarity NPC164194
0.542 Remote Similarity NPC478155
0.542 Remote Similarity NPC478154
0.5407 Remote Similarity NPC478598
0.5403 Remote Similarity NPC251768
0.5401 Remote Similarity NPC478153
0.5397 Remote Similarity NPC64715
0.5385 Remote Similarity NPC150893
0.5357 Remote Similarity NPC329960
0.5338 Remote Similarity NPC609305
0.5333 Remote Similarity NPC82380
0.5333 Remote Similarity NPC244296
0.5308 Remote Similarity NPC480936
0.5271 Remote Similarity NPC470477
0.5267 Remote Similarity NPC107536
0.5267 Remote Similarity NPC280029
0.5267 Remote Similarity NPC9470
0.5263 Remote Similarity NPC284449
0.5242 Remote Similarity NPC192791
0.5242 Remote Similarity NPC112352
0.5242 Remote Similarity NPC478066
0.5238 Remote Similarity NPC118440
0.5234 Remote Similarity NPC78034
0.5234 Remote Similarity NPC114484
0.5229 Remote Similarity NPC273668
0.5229 Remote Similarity NPC477473
0.5227 Remote Similarity NPC268184
0.5224 Remote Similarity NPC470476
0.5217 Remote Similarity NPC258617
0.5207 Remote Similarity NPC12288
0.5203 Remote Similarity NPC472949
0.52 Remote Similarity NPC114304
0.5197 Remote Similarity NPC470478
0.5194 Remote Similarity NPC301449
0.5194 Remote Similarity NPC601290
0.5188 Remote Similarity NPC151543
0.5159 Remote Similarity NPC164389
0.513 Remote Similarity NPC477469
0.513 Remote Similarity NPC477471
0.5122 Remote Similarity NPC127056
0.5115 Remote Similarity NPC36831
0.5109 Remote Similarity NPC4749
0.5098 Remote Similarity NPC477466
0.5081 Remote Similarity NPC488561
0.5079 Remote Similarity NPC480947
0.5078 Remote Similarity NPC257468
0.5078 Remote Similarity NPC123796
0.5076 Remote Similarity NPC477197
0.5075 Remote Similarity NPC123522
0.5074 Remote Similarity NPC269484
0.5074 Remote Similarity NPC97918
0.5072 Remote Similarity NPC134914
0.5041 Remote Similarity NPC56713
0.504 Remote Similarity NPC469946
0.5039 Remote Similarity NPC46665
0.5038 Remote Similarity NPC472267
0.5038 Remote Similarity NPC115656
0.5037 Remote Similarity NPC470911

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC30279 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