Natural Product: NPC166422

Natural Product IDNPC166422
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
3-O-Beta-D-Xylopyranosyl-(1->3)-Alpha-L-Rhamnopyranosyl-(1->2)-[Beta-D-Glucopyranosyl-(1->4)]-Alpha-L-Arabinopyranosyl Oleanolic Acid
IUPAC Name (4aS,6aR,6aS,6bR,8aR,10S,12aR,14bS)-10-[(2S,3R,4S,5S)-3-[(2S,3R,4R,5S,6S)-3,5-dihydroxy-6-methyl-4-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxy-4-hydroxy-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-2,2,6a,6b,9,9,12a-heptamethyl-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2430029
PubChem CID 73346237
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 YMUVECXYJPPWBW-ZQPXAOBSSA-N
Standard InCHI InChI=1S/C52H84O20/c1-23-32(55)40(71-42-37(60)33(56)26(54)21-65-42)39(62)44(67-23)72-41-35(58)28(69-43-38(61)36(59)34(57)27(20-53)68-43)22-66-45(41)70-31-12-13-49(6)29(48(31,4)5)11-14-51(8)30(49)10-9-24-25-19-47(2,3)15-17-52(25,46(63)64)18-16-50(24,51)7/h9,23,25-45,53-62H,10-22H2,1-8H3,(H,63,64)/t23-,25-,26+,27+,28-,29-,30+,31-,32-,33-,34+,35-,36-,37+,38+,39+,40+,41+,42-,43-,44-,45-,49-,50+,51+,52-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@H](CO[C@H]1O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC=C2[C@@H]4CC(C)(C)CC[C@@]4(CC[C@@]32C)C(=O)O)C1(C)C)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1028.56 Volume:   1001.471
?
Van der Waals volume.
Dense:   1.027 LogP:   1.474
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.214
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.259
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   51.0
TPSA:   313.44
?
Topological Polar Surface Area.
H-Bond Acceptor:   20.0
H-Bond Donor:   11.0 Rings:   9.0
Heavy Atoms:   20.0

MedChem Properties

QED Drug-Likeness Score:   0.107 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.638 Fsp3:   0.942
MCE-18:   192.653
?
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:   0.894 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.005
?
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:   0.233 Promiscuous compounds:   0.144

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.287 MDCK Permeability:   -5.232
Pgp-inhibitor:   0.0 Pgp-substrate:   0.032
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):   0.155
20% Bioavailability (F20%):   0.128 30% Bioavailability (F30%):   0.973
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.012 MRP1:   0.015
Plasma Protein Binding (PPB):   71.481% Volume Distribution (VD):   -0.429
Fu: 20.021%
?
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:   0.995 CYP3A4-substrate:   0.443
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.013
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):  -0.389 Half-life (T1/2):  3.95

ADMET: Toxicity

hERG Blockers:  0.006 hERG Blockers (10um):  0.005
Human Hepatotoxicity (H-HT):  0.772 Drug-induced Liver Injury (DILI):  0.978
AMES Toxicity:  0.861 Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.005 Skin Sensitization:  1.0
Carcinogencity:  0.06 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.003
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.999
Hematotoxicity:  0.535 Drug-induced Nephrotoxicity:  0.981
Genotoxicity:  0.048 RPMI-8226 Immunitoxicity:  0.153
A549 Cytotoxicity:  0.626 Hek293 Cytotoxicity:  0.395
BCF:   1.332
?
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:   3.81
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.449
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.533
?
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
NPO32682 anemone taipaiensis Species Ranunculaceae Eukaryota rhizomes n.a. n.a. PMID[23992864]
NPO32682 anemone taipaiensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT165 Cell line HeLa Homo sapiens IC50 = 7560.0 nM PubChem BioAssay data set
NPT81 Cell line A549 Homo sapiens IC50 = 8320.0 nM PMID[23398362]
NPT116 Cell line HL-60 Homo sapiens IC50 = 2370.0 nM PMID[22061825]
NPT65 Cell line HepG2 Homo sapiens IC50 = 5230.0 nM PMID[22365754]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 2250.0 nM PMID[23992864]

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 NPC166422 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
0.9327 High Similarity NPC323341
0.8716 High Similarity NPC54636
0.8704 High Similarity NPC219180
0.8661 High Similarity NPC471385
0.8654 High Similarity NPC324875
0.8654 High Similarity NPC292677
0.8611 High Similarity NPC471384
0.8544 High Similarity NPC257468
0.8365 Intermediate Similarity NPC481082
0.8365 Intermediate Similarity NPC164419
0.8037 Intermediate Similarity NPC276093
0.8036 Intermediate Similarity NPC251263
0.7925 Intermediate Similarity NPC139044
0.789 Intermediate Similarity NPC488564
0.7712 Intermediate Similarity NPC161717
0.7692 Intermediate Similarity NPC127056
0.7636 Intermediate Similarity NPC323359
0.7619 Intermediate Similarity NPC488561
0.757 Intermediate Similarity NPC114304
0.75 Intermediate Similarity NPC104400
0.75 Intermediate Similarity NPC475486
0.75 Intermediate Similarity NPC10320
0.7478 Intermediate Similarity NPC133818
0.7297 Intermediate Similarity NPC79718
0.7273 Intermediate Similarity NPC471383
0.7264 Intermediate Similarity NPC56713
0.7143 Intermediate Similarity NPC164194
0.7103 Intermediate Similarity NPC25605
0.7103 Intermediate Similarity NPC59804
0.7027 Intermediate Similarity NPC180550
0.7027 Intermediate Similarity NPC35405
0.6972 Remote Similarity NPC472949
0.6923 Remote Similarity NPC476992
0.6863 Remote Similarity NPC283849
0.6863 Remote Similarity NPC606107
0.6847 Remote Similarity NPC469945
0.6822 Remote Similarity NPC270667
0.6789 Remote Similarity NPC174679
0.6789 Remote Similarity NPC279554
0.678 Remote Similarity NPC288205
0.678 Remote Similarity NPC51465
0.6697 Remote Similarity NPC136877
0.6696 Remote Similarity NPC119794
0.6695 Remote Similarity NPC280941
0.6695 Remote Similarity NPC235772
0.6667 Remote Similarity NPC6377
0.6667 Remote Similarity NPC208381
0.6607 Remote Similarity NPC80843
0.6589 Remote Similarity NPC250247
0.6577 Remote Similarity NPC109079
0.6557 Remote Similarity NPC123199
0.6552 Remote Similarity NPC488515
0.6545 Remote Similarity NPC12288
0.6525 Remote Similarity NPC488209
0.6504 Remote Similarity NPC475140
0.6471 Remote Similarity NPC481078
0.6466 Remote Similarity NPC73829
0.646 Remote Similarity NPC22956
0.6406 Remote Similarity NPC136768
0.6393 Remote Similarity NPC79643
0.6381 Remote Similarity NPC28198
0.6381 Remote Similarity NPC476123
0.6311 Remote Similarity NPC473824
0.6286 Remote Similarity NPC204407
0.6283 Remote Similarity NPC114441
0.6228 Remote Similarity NPC488516
0.6202 Remote Similarity NPC43550
0.6148 Remote Similarity NPC62725
0.6129 Remote Similarity NPC151543
0.6111 Remote Similarity NPC191827
0.6098 Remote Similarity NPC475119
0.6071 Remote Similarity NPC40085
0.6055 Remote Similarity NPC100383
0.6048 Remote Similarity NPC610204
0.6033 Remote Similarity NPC291903
0.6015 Remote Similarity NPC488212
0.6 Remote Similarity NPC41061
0.6 Remote Similarity NPC227551
0.6 Remote Similarity NPC484832
0.595 Remote Similarity NPC37134
0.5935 Remote Similarity NPC609281
0.592 Remote Similarity NPC475287
0.5917 Remote Similarity NPC275668
0.5917 Remote Similarity NPC475504
0.5909 Remote Similarity NPC236638
0.5909 Remote Similarity NPC294453
0.5909 Remote Similarity NPC305981
0.5909 Remote Similarity NPC481081
0.5909 Remote Similarity NPC242611
0.5902 Remote Similarity NPC606145
0.5891 Remote Similarity NPC481080
0.5874 Remote Similarity NPC264270
0.5865 Remote Similarity NPC261506
0.5865 Remote Similarity NPC4328
0.5833 Remote Similarity NPC293330
0.5833 Remote Similarity NPC258885
0.5833 Remote Similarity NPC65105
0.5818 Remote Similarity NPC31839
0.5802 Remote Similarity NPC110633
0.5798 Remote Similarity NPC204392
0.5789 Remote Similarity NPC111466
0.5778 Remote Similarity NPC220160
0.5752 Remote Similarity NPC191410
0.5726 Remote Similarity NPC480424
0.5714 Remote Similarity NPC185466
0.5669 Remote Similarity NPC610461
0.5664 Remote Similarity NPC284807
0.5656 Remote Similarity NPC123796
0.5645 Remote Similarity NPC301449
0.5645 Remote Similarity NPC481079
0.5645 Remote Similarity NPC75318
0.5645 Remote Similarity NPC601290
0.5635 Remote Similarity NPC606553
0.563 Remote Similarity NPC302543
0.561 Remote Similarity NPC471435
0.561 Remote Similarity NPC471434
0.5574 Remote Similarity NPC63159
0.5556 Remote Similarity NPC202828
0.5556 Remote Similarity NPC119592
0.5547 Remote Similarity NPC607904
0.5538 Remote Similarity NPC603137
0.5536 Remote Similarity NPC286347
0.553 Remote Similarity NPC4749
0.5515 Remote Similarity NPC298034
0.5515 Remote Similarity NPC71065
0.5512 Remote Similarity NPC480939
0.55 Remote Similarity NPC213674
0.55 Remote Similarity NPC469946
0.5492 Remote Similarity NPC473383
0.5462 Remote Similarity NPC470911
0.5455 Remote Similarity NPC112352
0.5447 Remote Similarity NPC91838
0.5433 Remote Similarity NPC207738
0.5431 Remote Similarity NPC475472
0.5414 Remote Similarity NPC488211
0.5391 Remote Similarity NPC75287
0.5385 Remote Similarity NPC211798
0.5379 Remote Similarity NPC283417
0.5379 Remote Similarity NPC470218
0.5379 Remote Similarity NPC200049
0.5373 Remote Similarity NPC21691
0.5372 Remote Similarity NPC263756
0.5366 Remote Similarity NPC173859
0.5366 Remote Similarity NPC148603
0.5352 Remote Similarity NPC33012
0.5344 Remote Similarity NPC243680
0.5328 Remote Similarity NPC240734
0.5317 Remote Similarity NPC78034
0.5312 Remote Similarity NPC187290
0.5303 Remote Similarity NPC135904
0.5303 Remote Similarity NPC609305
0.5289 Remote Similarity NPC470512
0.5285 Remote Similarity NPC309714
0.5282 Remote Similarity NPC8524
0.528 Remote Similarity NPC297263
0.5271 Remote Similarity NPC11242
0.5259 Remote Similarity NPC57484
0.5254 Remote Similarity NPC127853
0.5252 Remote Similarity NPC70809
0.525 Remote Similarity NPC475296
0.5242 Remote Similarity NPC251768
0.5234 Remote Similarity NPC187618
0.5221 Remote Similarity NPC265841
0.5221 Remote Similarity NPC488308
0.5191 Remote Similarity NPC200788
0.5182 Remote Similarity NPC312650
0.5182 Remote Similarity NPC258617
0.5175 Remote Similarity NPC177246
0.5161 Remote Similarity NPC124296
0.5161 Remote Similarity NPC30289
0.5159 Remote Similarity NPC609763
0.5154 Remote Similarity NPC470915
0.5143 Remote Similarity NPC120840
0.5128 Remote Similarity NPC473538
0.512 Remote Similarity NPC164389
0.512 Remote Similarity NPC488526
0.5118 Remote Similarity NPC64715
0.5111 Remote Similarity NPC189575
0.5111 Remote Similarity NPC488560
0.5108 Remote Similarity NPC135849
0.5106 Remote Similarity NPC488309
0.5088 Remote Similarity NPC57362
0.5083 Remote Similarity NPC48499
0.5081 Remote Similarity NPC192791
0.5079 Remote Similarity NPC105800
0.5078 Remote Similarity NPC114484
0.5077 Remote Similarity NPC31838
0.5076 Remote Similarity NPC60557
0.5076 Remote Similarity NPC67857
0.5074 Remote Similarity NPC85154
0.5074 Remote Similarity NPC71391
0.5072 Remote Similarity NPC271610
0.5072 Remote Similarity NPC470876
0.5071 Remote Similarity NPC476991
0.5069 Remote Similarity NPC488210
0.5042 Remote Similarity NPC90856
0.5041 Remote Similarity NPC295371
0.504 Remote Similarity NPC160415
0.504 Remote Similarity NPC117714

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC166422 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