Natural Product: NPC304964

Natural Product IDNPC304964
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
SXLYHZXGNXAASM-VBSKCKADSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 163951
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 SXLYHZXGNXAASM-VBSKCKADSA-N
Standard InCHI InChI=1S/C55H88O22/c1-24-34(58)37(61)41(65)47(72-24)76-44-30(23-69-25(2)56)74-45(43(67)39(44)63)71-22-29-36(60)38(62)42(66)48(73-29)77-49(68)55-18-16-50(3,4)20-27(55)26-10-11-32-52(7)14-13-33(75-46-40(64)35(59)28(57)21-70-46)51(5,6)31(52)12-15-54(32,9)53(26,8)17-19-55/h10,24,27-48,57-67H,11-23H2,1-9H3/t24-,27-,28-,29+,30+,31-,32+,33-,34-,35-,36+,37+,38-,39+,40+,41+,42+,43+,44+,45+,46-,47-,48-,52-,53+,54+,55-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@@H](COC(=O)C)O[C@H]([C@@H]([C@H]1O)O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)OC(=O)[C@@]12CCC(C)(C)C[C@H]2C2=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]2(C)CC1)O[C@H]1[C@@H]([C@H]([C@H](CO1)O)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1100.58 Volume:   1068.303
?
Van der Waals volume.
Dense:   1.03 LogP:   1.933
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.743
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.622
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   13.0 Rigid Bonds:   52.0
TPSA:   339.74
?
Topological Polar Surface Area.
H-Bond Acceptor:   22.0
H-Bond Donor:   11.0 Rings:   9.0
Heavy Atoms:   22.0

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:   6.775 Fsp3:   0.927
MCE-18:   195.585
?
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:   0.927 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.009
?
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:   0.181 Promiscuous compounds:   0.136

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.26 MDCK Permeability:   -5.114
Pgp-inhibitor:   0.0 Pgp-substrate:   0.609
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):   0.229
20% Bioavailability (F20%):   0.799 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.016
Plasma Protein Binding (PPB):   68.21% Volume Distribution (VD):   -0.383
Fu: 17.426%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
BSEP inhibitor:   0.001

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:   0.959
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.991
HLM stability:   0.601
?
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):  -0.307 Half-life (T1/2):  3.178

ADMET: Toxicity

hERG Blockers:  0.003 hERG Blockers (10um):  0.021
Human Hepatotoxicity (H-HT):  0.568 Drug-induced Liver Injury (DILI):  0.842
AMES Toxicity:  0.922 Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.023 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.998
Hematotoxicity:  0.457 Drug-induced Nephrotoxicity:  0.993
Genotoxicity:  0.095 RPMI-8226 Immunitoxicity:  0.257
A549 Cytotoxicity:  0.735 Hek293 Cytotoxicity:  0.167
BCF:   1.502
?
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:   3.965
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.75
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.936
?
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
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. leaf n.a. PMID[17125224]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota leaves n.a. n.a. PMID[27400231]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11872 Eleutherococcus senticosus Species Araliaceae 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

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 NPC304964 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
0.8627 High Similarity NPC295823
0.8627 High Similarity NPC174720
0.8627 High Similarity NPC475467
0.7928 Intermediate Similarity NPC488560
0.7925 Intermediate Similarity NPC241909
0.7636 Intermediate Similarity NPC60557
0.7636 Intermediate Similarity NPC67857
0.7544 Intermediate Similarity NPC481080
0.7434 Intermediate Similarity NPC135904
0.7426 Intermediate Similarity NPC48499
0.7373 Intermediate Similarity NPC236638
0.7373 Intermediate Similarity NPC294453
0.7368 Intermediate Similarity NPC475160
0.7368 Intermediate Similarity NPC473714
0.7339 Intermediate Similarity NPC481079
0.7273 Intermediate Similarity NPC250247
0.7143 Intermediate Similarity NPC295371
0.7105 Intermediate Similarity NPC192600
0.7049 Intermediate Similarity NPC224381
0.7034 Intermediate Similarity NPC476068
0.7018 Intermediate Similarity NPC76972
0.7018 Intermediate Similarity NPC469782
0.7018 Intermediate Similarity NPC204414
0.6972 Remote Similarity NPC63159
0.6944 Remote Similarity NPC104071
0.6942 Remote Similarity NPC305981
0.6942 Remote Similarity NPC481081
0.693 Remote Similarity NPC114287
0.6885 Remote Similarity NPC261506
0.6885 Remote Similarity NPC4328
0.6881 Remote Similarity NPC102439
0.686 Remote Similarity NPC43550
0.6838 Remote Similarity NPC123199
0.6803 Remote Similarity NPC202828
0.6803 Remote Similarity NPC119592
0.6777 Remote Similarity NPC41061
0.6777 Remote Similarity NPC227551
0.6777 Remote Similarity NPC258617
0.6697 Remote Similarity NPC112352
0.6695 Remote Similarity NPC155410
0.6667 Remote Similarity NPC148417
0.6667 Remote Similarity NPC79643
0.661 Remote Similarity NPC165204
0.6606 Remote Similarity NPC76497
0.6606 Remote Similarity NPC469946
0.6518 Remote Similarity NPC235438
0.65 Remote Similarity NPC100639
0.6481 Remote Similarity NPC235405
0.6475 Remote Similarity NPC57484
0.6434 Remote Similarity NPC480422
0.6429 Remote Similarity NPC70809
0.6429 Remote Similarity NPC46665
0.6422 Remote Similarity NPC249848
0.6422 Remote Similarity NPC107966
0.6415 Remote Similarity NPC90856
0.6349 Remote Similarity NPC309223
0.6349 Remote Similarity NPC298034
0.6349 Remote Similarity NPC71065
0.6325 Remote Similarity NPC31838
0.6325 Remote Similarity NPC481078
0.6325 Remote Similarity NPC187290
0.632 Remote Similarity NPC65105
0.6316 Remote Similarity NPC297263
0.629 Remote Similarity NPC110633
0.627 Remote Similarity NPC136768
0.6216 Remote Similarity NPC39211
0.6204 Remote Similarity NPC29069
0.6195 Remote Similarity NPC30735
0.6182 Remote Similarity NPC475516
0.6154 Remote Similarity NPC102505
0.6154 Remote Similarity NPC301449
0.6154 Remote Similarity NPC488514
0.6154 Remote Similarity NPC601290
0.6148 Remote Similarity NPC309907
0.6148 Remote Similarity NPC480419
0.614 Remote Similarity NPC488526
0.6132 Remote Similarity NPC128925
0.6126 Remote Similarity NPC173583
0.6124 Remote Similarity NPC220160
0.6111 Remote Similarity NPC214484
0.6111 Remote Similarity NPC475514
0.6098 Remote Similarity NPC470218
0.6032 Remote Similarity NPC13998
0.6031 Remote Similarity NPC480417
0.5982 Remote Similarity NPC473373
0.5942 Remote Similarity NPC297950
0.5938 Remote Similarity NPC293330
0.5932 Remote Similarity NPC104372
0.5932 Remote Similarity NPC114484
0.5917 Remote Similarity NPC473826
0.5909 Remote Similarity NPC1046
0.5906 Remote Similarity NPC480418
0.5899 Remote Similarity NPC472268
0.5897 Remote Similarity NPC222580
0.5854 Remote Similarity NPC123522
0.5841 Remote Similarity NPC480420
0.5833 Remote Similarity NPC80986
0.5826 Remote Similarity NPC223301
0.5826 Remote Similarity NPC171544
0.5822 Remote Similarity NPC469776
0.5818 Remote Similarity NPC204458
0.5812 Remote Similarity NPC105800
0.5812 Remote Similarity NPC475591
0.5812 Remote Similarity NPC236870
0.5798 Remote Similarity NPC281148
0.5785 Remote Similarity NPC104137
0.5785 Remote Similarity NPC26626
0.5781 Remote Similarity NPC286457
0.5772 Remote Similarity NPC475287
0.5766 Remote Similarity NPC78046
0.5726 Remote Similarity NPC40775
0.5726 Remote Similarity NPC10607
0.5726 Remote Similarity NPC251768
0.5726 Remote Similarity NPC164389
0.5726 Remote Similarity NPC101744
0.5726 Remote Similarity NPC473459
0.5667 Remote Similarity NPC481323
0.5652 Remote Similarity NPC157868
0.5615 Remote Similarity NPC470876
0.5608 Remote Similarity NPC472269
0.5603 Remote Similarity NPC263756
0.5603 Remote Similarity NPC213674
0.56 Remote Similarity NPC32723
0.5593 Remote Similarity NPC159309
0.5593 Remote Similarity NPC232237
0.5593 Remote Similarity NPC86222
0.5583 Remote Similarity NPC134835
0.5574 Remote Similarity NPC96641
0.5574 Remote Similarity NPC163183
0.5563 Remote Similarity NPC469778
0.5556 Remote Similarity NPC192791
0.5545 Remote Similarity NPC256798
0.5517 Remote Similarity NPC488516
0.5512 Remote Similarity NPC475209
0.5508 Remote Similarity NPC160415
0.549 Remote Similarity NPC135334
0.5489 Remote Similarity NPC302543
0.5486 Remote Similarity NPC45606
0.547 Remote Similarity NPC473343
0.547 Remote Similarity NPC161674
0.5462 Remote Similarity NPC173859
0.5462 Remote Similarity NPC148603
0.5462 Remote Similarity NPC480475
0.5455 Remote Similarity NPC481324
0.5433 Remote Similarity NPC475899
0.541 Remote Similarity NPC73318
0.54 Remote Similarity NPC469775
0.5385 Remote Similarity NPC85154
0.537 Remote Similarity NPC237503
0.5349 Remote Similarity NPC191827
0.5345 Remote Similarity NPC139894
0.5333 Remote Similarity NPC104400
0.5333 Remote Similarity NPC10320
0.5327 Remote Similarity NPC167383
0.5319 Remote Similarity NPC475368
0.5316 Remote Similarity NPC295941
0.5303 Remote Similarity NPC473452
0.5289 Remote Similarity NPC68175
0.5285 Remote Similarity NPC37134
0.5263 Remote Similarity NPC189884
0.5263 Remote Similarity NPC138334
0.5252 Remote Similarity NPC8524
0.525 Remote Similarity NPC469773
0.525 Remote Similarity NPC117714
0.525 Remote Similarity NPC309714
0.525 Remote Similarity NPC30289
0.5238 Remote Similarity NPC11242
0.5231 Remote Similarity NPC283417
0.5231 Remote Similarity NPC480423
0.5231 Remote Similarity NPC200049
0.5227 Remote Similarity NPC21691
0.5214 Remote Similarity NPC33012
0.5203 Remote Similarity NPC488515
0.5203 Remote Similarity NPC484832
0.5203 Remote Similarity NPC601659
0.5195 Remote Similarity NPC469774
0.5175 Remote Similarity NPC489208
0.5169 Remote Similarity NPC150400
0.5159 Remote Similarity NPC207738
0.5156 Remote Similarity NPC300419
0.5156 Remote Similarity NPC610204
0.5152 Remote Similarity NPC4749
0.5135 Remote Similarity NPC220838
0.5126 Remote Similarity NPC473884
0.5126 Remote Similarity NPC470512
0.5124 Remote Similarity NPC109588
0.5122 Remote Similarity NPC475504
0.5122 Remote Similarity NPC609763
0.5115 Remote Similarity NPC471550
0.5113 Remote Similarity NPC473386
0.5111 Remote Similarity NPC161717
0.5096 Remote Similarity NPC100925
0.5088 Remote Similarity NPC209894
0.5079 Remote Similarity NPC480473
0.5079 Remote Similarity NPC480474
0.5078 Remote Similarity NPC185466
0.5077 Remote Similarity NPC470911
0.5072 Remote Similarity NPC478823
0.5043 Remote Similarity NPC161434
0.5042 Remote Similarity NPC58448

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC304964 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