Natural Product: NPC295823

Natural Product IDNPC295823
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
28-O-Alpha-L-Rhamnopyranosyl-(1->4)-O-Beta-D-Glucopyranosyl-(1->6)-O-Beta-D-Glucopyranosyloleanate 3-O-Beta-D-Xylopyranoside
IUPAC Name [(2S,3R,4S,5S,6R)-6-[[(2R,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxymethyl]-3,4,5-trihydroxyoxan-2-yl] (4aS,6aR,6aS,6bR,8aR,10S,12aR,14bS)-2,2,6a,6b,9,9,12a-heptamethyl-10-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2391933
PubChem CID 71697453
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 XPZZGRWYXQODIS-DONWFASLSA-N
Standard InCHI InChI=1S/C53H86O21/c1-23-32(56)35(59)39(63)45(69-23)73-42-27(20-54)70-43(41(65)37(42)61)68-22-28-34(58)36(60)40(64)46(71-28)74-47(66)53-17-15-48(2,3)19-25(53)24-9-10-30-50(6)13-12-31(72-44-38(62)33(57)26(55)21-67-44)49(4,5)29(50)11-14-52(30,8)51(24,7)16-18-53/h9,23,25-46,54-65H,10-22H2,1-8H3/t23-,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-/m0/s1
SMILES OC[C@H]1O[C@@H](OC[C@H]2O[C@@H](OC(=O)[C@]34CC[C@@]5(C(=CC[C@H]6[C@@]5(C)CC[C@@H]5[C@]6(C)CC[C@@H](C5(C)C)O[C@@H]5OC[C@H]([C@@H]([C@H]5O)O)O)[C@@H]4CC(CC3)(C)C)C)[C@@H]([C@H]([C@@H]2O)O)O)[C@@H]([C@H]([C@@H]1O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1058.57 Volume:   1027.557
?
Van der Waals volume.
Dense:   1.03 LogP:   1.745
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.513
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.411
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   51.0
TPSA:   333.67
?
Topological Polar Surface Area.
H-Bond Acceptor:   21.0
H-Bond Donor:   12.0 Rings:   9.0
Heavy Atoms:   21.0

MedChem Properties

QED Drug-Likeness Score:   0.075 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.693 Fsp3:   0.943
MCE-18:   194.369
?
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:   0.883 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.008
?
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:   0.203 Promiscuous compounds:   0.067

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.422 MDCK Permeability:   -5.11
Pgp-inhibitor:   0.0 Pgp-substrate:   0.37
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):   0.988
20% Bioavailability (F20%):   0.935 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.023 MRP1:   0.002
Plasma Protein Binding (PPB):   68.845% Volume Distribution (VD):   -0.308
Fu: 16.264%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.002
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.005 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:   0.991
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.419
HLM stability:   0.044
?
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):  -0.411 Half-life (T1/2):  3.816

ADMET: Toxicity

hERG Blockers:  0.004 hERG Blockers (10um):  0.008
Human Hepatotoxicity (H-HT):  0.701 Drug-induced Liver Injury (DILI):  0.933
AMES Toxicity:  0.917 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.002 Skin Sensitization:  1.0
Carcinogencity:  0.025 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.447 Drug-induced Nephrotoxicity:  0.998
Genotoxicity:  0.166 RPMI-8226 Immunitoxicity:  0.29
A549 Cytotoxicity:  0.741 Hek293 Cytotoxicity:  0.2
BCF:   1.84
?
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:   3.951
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.418
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.643
?
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
NPO25457 Anemone anhuiensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25457 Anemone anhuiensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25457 Anemone anhuiensis Species Ranunculaceae 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
NPT1083 Cell line A-375 Homo sapiens IC50 = 13500.0 nM PMID[23639650]
NPT81 Cell line A549 Homo sapiens IC50 = 11900.0 nM PMID[23639650]
NPT116 Cell line HL-60 Homo sapiens IC50 = 5700.0 nM PMID[23639650]

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 NPC295823 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 NPC174720
1.0 High Similarity NPC475467
0.9184 High Similarity NPC241909
0.9126 High Similarity NPC488560
0.8824 High Similarity NPC60557
0.8824 High Similarity NPC67857
0.8679 High Similarity NPC481080
0.8571 High Similarity NPC135904
0.8491 Intermediate Similarity NPC475160
0.8491 Intermediate Similarity NPC473714
0.8455 Intermediate Similarity NPC236638
0.8455 Intermediate Similarity NPC294453
0.8158 Intermediate Similarity NPC250247
0.8113 Intermediate Similarity NPC76972
0.8113 Intermediate Similarity NPC469782
0.8113 Intermediate Similarity NPC204414
0.81 Intermediate Similarity NPC104071
0.8091 Intermediate Similarity NPC476068
0.802 Intermediate Similarity NPC102439
0.7965 Intermediate Similarity NPC305981
0.7938 Intermediate Similarity NPC48499
0.7895 Intermediate Similarity NPC261506
0.7895 Intermediate Similarity NPC4328
0.787 Intermediate Similarity NPC192600
0.781 Intermediate Similarity NPC481079
0.7807 Intermediate Similarity NPC202828
0.7807 Intermediate Similarity NPC119592
0.7788 Intermediate Similarity NPC41061
0.7788 Intermediate Similarity NPC227551
0.7788 Intermediate Similarity NPC258617
0.7767 Intermediate Similarity NPC148417
0.7719 Intermediate Similarity NPC43550
0.7636 Intermediate Similarity NPC165204
0.7624 Intermediate Similarity NPC295371
0.7568 Intermediate Similarity NPC155410
0.75 Intermediate Similarity NPC100639
0.7429 Intermediate Similarity NPC63159
0.735 Intermediate Similarity NPC481081
0.7288 Intermediate Similarity NPC298034
0.7288 Intermediate Similarity NPC71065
0.7257 Intermediate Similarity NPC123199
0.7241 Intermediate Similarity NPC110633
0.7167 Intermediate Similarity NPC224381
0.7155 Intermediate Similarity NPC57484
0.7143 Intermediate Similarity NPC112352
0.7119 Intermediate Similarity NPC65105
0.708 Intermediate Similarity NPC79643
0.7059 Intermediate Similarity NPC136768
0.7048 Intermediate Similarity NPC469946
0.6923 Remote Similarity NPC235405
0.6891 Remote Similarity NPC475514
0.6885 Remote Similarity NPC220160
0.6875 Remote Similarity NPC473826
0.6863 Remote Similarity NPC90856
0.6857 Remote Similarity NPC249848
0.6857 Remote Similarity NPC107966
0.6852 Remote Similarity NPC46665
0.6803 Remote Similarity NPC70809
0.6789 Remote Similarity NPC235438
0.6727 Remote Similarity NPC297263
0.6726 Remote Similarity NPC481078
0.6726 Remote Similarity NPC187290
0.6697 Remote Similarity NPC101744
0.6696 Remote Similarity NPC475287
0.6667 Remote Similarity NPC480422
0.6635 Remote Similarity NPC29069
0.6606 Remote Similarity NPC30735
0.6604 Remote Similarity NPC475516
0.6579 Remote Similarity NPC31838
0.6569 Remote Similarity NPC128925
0.6549 Remote Similarity NPC301449
0.6549 Remote Similarity NPC601290
0.6538 Remote Similarity NPC214484
0.6481 Remote Similarity NPC39211
0.6475 Remote Similarity NPC469776
0.6471 Remote Similarity NPC470218
0.6389 Remote Similarity NPC473373
0.6372 Remote Similarity NPC134835
0.6356 Remote Similarity NPC123522
0.6338 Remote Similarity NPC32723
0.632 Remote Similarity NPC309223
0.6316 Remote Similarity NPC114484
0.6294 Remote Similarity NPC481323
0.6294 Remote Similarity NPC469778
0.629 Remote Similarity NPC293330
0.626 Remote Similarity NPC286457
0.625 Remote Similarity NPC475209
0.6226 Remote Similarity NPC204458
0.6216 Remote Similarity NPC223301
0.6216 Remote Similarity NPC171544
0.6207 Remote Similarity NPC135334
0.6195 Remote Similarity NPC475591
0.6195 Remote Similarity NPC236870
0.6174 Remote Similarity NPC281148
0.6174 Remote Similarity NPC73318
0.6174 Remote Similarity NPC104372
0.6168 Remote Similarity NPC1046
0.6168 Remote Similarity NPC78046
0.6164 Remote Similarity NPC481324
0.614 Remote Similarity NPC222580
0.6126 Remote Similarity NPC76497
0.6124 Remote Similarity NPC102505
0.6124 Remote Similarity NPC480417
0.6124 Remote Similarity NPC488514
0.6116 Remote Similarity NPC480419
0.6106 Remote Similarity NPC40775
0.6106 Remote Similarity NPC10607
0.6106 Remote Similarity NPC251768
0.6106 Remote Similarity NPC488526
0.6103 Remote Similarity NPC472268
0.608 Remote Similarity NPC470876
0.6068 Remote Similarity NPC80986
0.6036 Remote Similarity NPC157868
0.6029 Remote Similarity NPC297950
0.6017 Remote Similarity NPC104137
0.6017 Remote Similarity NPC26626
0.6014 Remote Similarity NPC469775
0.6 Remote Similarity NPC480418
0.6 Remote Similarity NPC13998
0.6 Remote Similarity NPC295941
0.5982 Remote Similarity NPC263756
0.5982 Remote Similarity NPC213674
0.5965 Remote Similarity NPC159309
0.5965 Remote Similarity NPC164389
0.5965 Remote Similarity NPC473459
0.5965 Remote Similarity NPC86222
0.5948 Remote Similarity NPC601659
0.5946 Remote Similarity NPC173583
0.5943 Remote Similarity NPC256798
0.5929 Remote Similarity NPC192791
0.5917 Remote Similarity NPC114287
0.5906 Remote Similarity NPC161717
0.589 Remote Similarity NPC469774
0.5877 Remote Similarity NPC160415
0.5841 Remote Similarity NPC161674
0.5826 Remote Similarity NPC173859
0.5826 Remote Similarity NPC148603
0.5826 Remote Similarity NPC480475
0.5812 Remote Similarity NPC469821
0.5804 Remote Similarity NPC480420
0.5786 Remote Similarity NPC45606
0.5776 Remote Similarity NPC105800
0.5772 Remote Similarity NPC475899
0.5772 Remote Similarity NPC100925
0.5769 Remote Similarity NPC237503
0.5748 Remote Similarity NPC473452
0.5728 Remote Similarity NPC167383
0.5702 Remote Similarity NPC473343
0.5695 Remote Similarity NPC469777
0.5692 Remote Similarity NPC302543
0.5685 Remote Similarity NPC472269
0.5641 Remote Similarity NPC68175
0.5636 Remote Similarity NPC189884
0.5636 Remote Similarity NPC138334
0.562 Remote Similarity NPC475368
0.5591 Remote Similarity NPC85154
0.5584 Remote Similarity NPC469772
0.5575 Remote Similarity NPC139894
0.5556 Remote Similarity NPC232237
0.5556 Remote Similarity NPC191827
0.5513 Remote Similarity NPC469773
0.5478 Remote Similarity NPC473884
0.5478 Remote Similarity NPC470512
0.5478 Remote Similarity NPC488516
0.547 Remote Similarity NPC109588
0.547 Remote Similarity NPC117714
0.547 Remote Similarity NPC309714
0.547 Remote Similarity NPC30289
0.5462 Remote Similarity NPC475504
0.5455 Remote Similarity NPC209894
0.5447 Remote Similarity NPC11242
0.5441 Remote Similarity NPC8524
0.5433 Remote Similarity NPC283417
0.5433 Remote Similarity NPC471550
0.5433 Remote Similarity NPC200049
0.5426 Remote Similarity NPC21691
0.5424 Remote Similarity NPC104400
0.5424 Remote Similarity NPC10320
0.5417 Remote Similarity NPC220838
0.541 Remote Similarity NPC96641
0.541 Remote Similarity NPC480473
0.541 Remote Similarity NPC163183
0.541 Remote Similarity NPC480474
0.5405 Remote Similarity NPC161434
0.5401 Remote Similarity NPC33012
0.5391 Remote Similarity NPC58448
0.5391 Remote Similarity NPC47995
0.5391 Remote Similarity NPC150400
0.5385 Remote Similarity NPC242840
0.5366 Remote Similarity NPC207738
0.536 Remote Similarity NPC300419
0.5357 Remote Similarity NPC489208
0.5349 Remote Similarity NPC4749
0.5333 Remote Similarity NPC609763
0.5289 Remote Similarity NPC484832
0.5276 Remote Similarity NPC470911
0.525 Remote Similarity NPC470515
0.5246 Remote Similarity NPC37134
0.5242 Remote Similarity NPC36831

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC295823 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