Natural Product: NPC471384

Natural Product IDNPC471384
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
3 Beta-O-{Beta-D-Xylopyranosyl-(1->3)-Alpha-L-Rhamnopyranosyl-(1->2)-[Beta-D-Glucopyranosyl-(1->4)]-Alpha-L-Arabinopyranosyl}Siaresinolic Acid
IUPAC Name (1S,4aR,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-1-hydroxy-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 CHEMBL2430036
PubChem CID 72189837
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 YYNGQYRUWXEJIJ-ZNTOFBKISA-N
Standard InCHI InChI=1S/C52H84O21/c1-22-31(55)39(72-42-36(60)32(56)24(54)20-66-42)38(62)44(68-22)73-40-34(58)26(70-43-37(61)35(59)33(57)25(19-53)69-43)21-67-45(40)71-29-12-13-49(6)27(48(29,4)5)11-14-51(8)28(49)10-9-23-30-41(63)47(2,3)15-17-52(30,46(64)65)18-16-50(23,51)7/h9,22,24-45,53-63H,10-21H2,1-8H3,(H,64,65)/t22-,24+,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 CC1C(C(C(C(O1)OC2C(C(COC2OC3CCC4(C(C3(C)C)CCC5(C4CC=C6C5(CCC7(C6C(C(CC7)(C)C)O)C(=O)O)C)C)C)OC8C(C(C(C(O8)CO)O)O)O)O)O)OC9C(C(C(CO9)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1044.55 Volume:   1010.261
?
Van der Waals volume.
Dense:   1.034 LogP:   0.376
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.386
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.342
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 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:   0.1 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.74 Fsp3:   0.942
MCE-18:   195.446
?
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:   0.021 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:   0.392
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.33 Promiscuous compounds:   0.001

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.788 MDCK Permeability:   -4.835
Pgp-inhibitor:   0.0 Pgp-substrate:   0.997
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%):   0.481 30% Bioavailability (F30%):   0.991
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   1.0
Plasma Protein Binding (PPB):   43.388% Volume Distribution (VD):   -0.469
Fu: 30.944%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.0
OATP1B3 inhibitor:   0.036 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.999 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.998 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.208 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
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):  -0.369 Half-life (T1/2):  3.877

ADMET: Toxicity

hERG Blockers:  0.011 hERG Blockers (10um):  0.147
Human Hepatotoxicity (H-HT):  0.263 Drug-induced Liver Injury (DILI):  0.221
AMES Toxicity:  0.186 Rat Oral Acute Toxicity:  0.109
Maximum Recommended Daily Dose:  0.328 Skin Sensitization:  0.007
Carcinogencity:  0.004 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.241 Ototoxicity:  1.0
Hematotoxicity:  0.006 Drug-induced Nephrotoxicity:  0.03
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.069
A549 Cytotoxicity:  0.022 Hek293 Cytotoxicity:  0.664
BCF:   0.559
?
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:   4.134
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.227
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.177
?
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 > 80000.0 nM PMID[18676884]
NPT81 Cell line A549 Homo sapiens IC50 = 53140.0 nM PMID[23190013]
NPT116 Cell line HL-60 Homo sapiens IC50 = 38640.0 nM PMID[23665143]
NPT65 Cell line HepG2 Homo sapiens IC50 = 35720.0 nM DrugMatrix in vitro pharmacology data
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 57280.0 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 NPC471384 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
0.8611 High Similarity NPC166422
0.8018 Intermediate Similarity NPC323341
0.75 Intermediate Similarity NPC54636
0.7479 Intermediate Similarity NPC471385
0.7478 Intermediate Similarity NPC219180
0.7387 Intermediate Similarity NPC324875
0.7387 Intermediate Similarity NPC292677
0.7273 Intermediate Similarity NPC257468
0.7117 Intermediate Similarity NPC481082
0.7117 Intermediate Similarity NPC164419
0.6891 Remote Similarity NPC251263
0.6842 Remote Similarity NPC276093
0.6726 Remote Similarity NPC139044
0.6724 Remote Similarity NPC488564
0.672 Remote Similarity NPC136768
0.6667 Remote Similarity NPC475486
0.664 Remote Similarity NPC161717
0.6557 Remote Similarity NPC475140
0.6496 Remote Similarity NPC323359
0.6486 Remote Similarity NPC127056
0.6429 Remote Similarity NPC488561
0.6404 Remote Similarity NPC114304
0.6393 Remote Similarity NPC133818
0.6385 Remote Similarity NPC250247
0.6348 Remote Similarity NPC104400
0.6348 Remote Similarity NPC10320
0.6341 Remote Similarity NPC123199
0.625 Remote Similarity NPC481078
0.623 Remote Similarity NPC473824
0.6186 Remote Similarity NPC79718
0.6179 Remote Similarity NPC151543
0.6179 Remote Similarity NPC79643
0.6154 Remote Similarity NPC471383
0.6106 Remote Similarity NPC56713
0.6094 Remote Similarity NPC110633
0.6016 Remote Similarity NPC475119
0.6016 Remote Similarity NPC288205
0.6016 Remote Similarity NPC51465
0.6 Remote Similarity NPC43550
0.5982 Remote Similarity NPC164194
0.5968 Remote Similarity NPC610204
0.5966 Remote Similarity NPC275668
0.5965 Remote Similarity NPC25605
0.5965 Remote Similarity NPC59804
0.595 Remote Similarity NPC291903
0.5932 Remote Similarity NPC180550
0.5932 Remote Similarity NPC35405
0.5917 Remote Similarity NPC484832
0.5906 Remote Similarity NPC191827
0.5887 Remote Similarity NPC476992
0.5882 Remote Similarity NPC258885
0.5868 Remote Similarity NPC37134
0.5862 Remote Similarity NPC472949
0.5854 Remote Similarity NPC609281
0.5847 Remote Similarity NPC204392
0.582 Remote Similarity NPC606145
0.5812 Remote Similarity NPC80843
0.5802 Remote Similarity NPC41061
0.5802 Remote Similarity NPC227551
0.5785 Remote Similarity NPC488515
0.5775 Remote Similarity NPC40085
0.5763 Remote Similarity NPC469945
0.576 Remote Similarity NPC185466
0.5714 Remote Similarity NPC475287
0.5714 Remote Similarity NPC236638
0.5714 Remote Similarity NPC294453
0.5714 Remote Similarity NPC305981
0.5714 Remote Similarity NPC481081
0.5704 Remote Similarity NPC488212
0.5702 Remote Similarity NPC270667
0.5702 Remote Similarity NPC475504
0.5702 Remote Similarity NPC123796
0.5692 Remote Similarity NPC481080
0.569 Remote Similarity NPC174679
0.569 Remote Similarity NPC279554
0.5688 Remote Similarity NPC283849
0.5688 Remote Similarity NPC606107
0.568 Remote Similarity NPC280941
0.568 Remote Similarity NPC235772
0.568 Remote Similarity NPC606553
0.5672 Remote Similarity NPC261506
0.5672 Remote Similarity NPC4328
0.5656 Remote Similarity NPC471435
0.5656 Remote Similarity NPC471434
0.5656 Remote Similarity NPC119794
0.5639 Remote Similarity NPC65105
0.5625 Remote Similarity NPC470911
0.5603 Remote Similarity NPC136877
0.5593 Remote Similarity NPC6377
0.5593 Remote Similarity NPC208381
0.5591 Remote Similarity NPC610461
0.5588 Remote Similarity NPC220160
0.5586 Remote Similarity NPC264270
0.5581 Remote Similarity NPC603137
0.5537 Remote Similarity NPC173859
0.5537 Remote Similarity NPC148603
0.5522 Remote Similarity NPC293330
0.552 Remote Similarity NPC488209
0.5508 Remote Similarity NPC109079
0.5492 Remote Similarity NPC91838
0.5481 Remote Similarity NPC111466
0.5476 Remote Similarity NPC207738
0.547 Remote Similarity NPC12288
0.5469 Remote Similarity NPC607904
0.5462 Remote Similarity NPC470512
0.5462 Remote Similarity NPC488516
0.5447 Remote Similarity NPC73829
0.5441 Remote Similarity NPC302543
0.544 Remote Similarity NPC301449
0.544 Remote Similarity NPC481079
0.544 Remote Similarity NPC601290
0.5431 Remote Similarity NPC211798
0.5417 Remote Similarity NPC22956
0.5372 Remote Similarity NPC240734
0.5368 Remote Similarity NPC202828
0.5368 Remote Similarity NPC119592
0.5366 Remote Similarity NPC63159
0.536 Remote Similarity NPC78034
0.5344 Remote Similarity NPC609305
0.5338 Remote Similarity NPC4749
0.5328 Remote Similarity NPC298034
0.5328 Remote Similarity NPC71065
0.5328 Remote Similarity NPC309714
0.5312 Remote Similarity NPC470915
0.5289 Remote Similarity NPC213674
0.5289 Remote Similarity NPC469946
0.5268 Remote Similarity NPC28198
0.5268 Remote Similarity NPC476123
0.5267 Remote Similarity NPC243680
0.525 Remote Similarity NPC114441
0.5246 Remote Similarity NPC112352
0.5221 Remote Similarity NPC177246
0.5217 Remote Similarity NPC128925
0.5203 Remote Similarity NPC124296
0.5194 Remote Similarity NPC75287
0.5194 Remote Similarity NPC62725
0.5188 Remote Similarity NPC283417
0.5188 Remote Similarity NPC470218
0.5188 Remote Similarity NPC200049
0.5185 Remote Similarity NPC21691
0.5179 Remote Similarity NPC204407
0.5164 Remote Similarity NPC263756
0.5156 Remote Similarity NPC187618
0.5147 Remote Similarity NPC265841
0.5147 Remote Similarity NPC488308
0.5133 Remote Similarity NPC57362
0.513 Remote Similarity NPC242611
0.512 Remote Similarity NPC105800
0.512 Remote Similarity NPC470515
0.5116 Remote Similarity NPC187290
0.5115 Remote Similarity NPC200788
0.5113 Remote Similarity NPC135904
0.5111 Remote Similarity NPC488211
0.5109 Remote Similarity NPC271610
0.5109 Remote Similarity NPC312650
0.5085 Remote Similarity NPC90856
0.5081 Remote Similarity NPC160415
0.5079 Remote Similarity NPC470513
0.5079 Remote Similarity NPC297263
0.5077 Remote Similarity NPC11242
0.5074 Remote Similarity NPC57484
0.5071 Remote Similarity NPC70809
0.5069 Remote Similarity NPC33012
0.5065 Remote Similarity NPC478559
0.5065 Remote Similarity NPC478560
0.5043 Remote Similarity NPC31839
0.5041 Remote Similarity NPC108748
0.504 Remote Similarity NPC251768
0.504 Remote Similarity NPC473383
0.5038 Remote Similarity NPC284449
0.5037 Remote Similarity NPC189575
0.5035 Remote Similarity NPC488309

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471384 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