Natural Product: NPC165204

Natural Product IDNPC165204
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
UPROOJBJZLZCGS-CHTHVDMYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 195123
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001755] Diterpene glycosides

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 UPROOJBJZLZCGS-CHTHVDMYSA-N
Standard InCHI InChI=1S/C58H92O25/c1-23-11-16-58(53(73)83-51-44(71)40(67)37(64)30(79-51)22-75-48-45(72)41(68)46(29(20-59)78-48)81-49-42(69)38(65)34(61)24(2)76-49)18-17-56(7)26(27(58)19-23)9-10-32-55(6)14-13-33(54(4,5)31(55)12-15-57(32,56)8)80-52-47(36(63)28(60)21-74-52)82-50-43(70)39(66)35(62)25(3)77-50/h9,24-25,27-52,59-72H,1,10-22H2,2-8H3/t24-,25-,27-,28-,29+,30+,31-,32+,33-,34-,35-,36-,37+,38+,39+,40-,41+,42+,43+,44+,45+,46+,47+,48+,49-,50-,51-,52-,55-,56+,57+,58-/m0/s1
SMILES C=C1CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]34C)O[C@H]3[C@@H]([C@H]([C@H](CO3)O)O)O[C@H]3[C@@H]([C@@H]([C@H]([C@H](C)O3)O)O)O)[C@@H]2C1)C(=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O)O)O)O)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1188.59 Volume:   1138.005
?
Van der Waals volume.
Dense:   1.044 LogP:   0.527
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.263
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.374
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   13.0 Rigid Bonds:   58.0
TPSA:   392.59
?
Topological Polar Surface Area.
H-Bond Acceptor:   25.0
H-Bond Donor:   14.0 Rings:   10.0
Heavy Atoms:   25.0

MedChem Properties

QED Drug-Likeness Score:   0.057 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.214 Fsp3:   0.914
MCE-18:   212.252
?
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:   0.808 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.006
?
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:   0.287 Promiscuous compounds:   0.09

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.63 MDCK Permeability:   -4.921
Pgp-inhibitor:   0.0 Pgp-substrate:   0.976
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):   0.524
20% Bioavailability (F20%):   0.698 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.138
Plasma Protein Binding (PPB):   57.683% Volume Distribution (VD):   -0.321
Fu: 25.744%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.999 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:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.543
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):  -0.549 Half-life (T1/2):  4.12

ADMET: Toxicity

hERG Blockers:  0.002 hERG Blockers (10um):  0.009
Human Hepatotoxicity (H-HT):  0.416 Drug-induced Liver Injury (DILI):  0.912
AMES Toxicity:  0.981 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.002 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.503 Drug-induced Nephrotoxicity:  0.995
Genotoxicity:  0.145 RPMI-8226 Immunitoxicity:  0.43
A549 Cytotoxicity:  0.883 Hek293 Cytotoxicity:  0.286
BCF:   1.611
?
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:   3.623
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.08
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.285
?
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
NPO26193 Piper methysticum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[11830162]
NPO26193 Piper methysticum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[12809361]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. leaf n.a. PMID[17125224]
NPO26193 Piper methysticum Species Piperaceae Eukaryota root n.a. n.a. PMID[25597012]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota leaves n.a. n.a. PMID[27400231]
NPO26193 Piper methysticum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26193 Piper methysticum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26193 Piper methysticum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26193 Piper methysticum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26193 Piper methysticum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
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
NPT967 Individual protein Xanthine dehydrogenase Homo sapiens IC50 = 97300.0 nM PMID[28511908]

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 NPC165204 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
0.8679 High Similarity NPC60557
0.8679 High Similarity NPC67857
0.844 Intermediate Similarity NPC135904
0.8 Intermediate Similarity NPC76972
0.8 Intermediate Similarity NPC469782
0.8 Intermediate Similarity NPC204414
0.7863 Intermediate Similarity NPC236638
0.7863 Intermediate Similarity NPC294453
0.7863 Intermediate Similarity NPC305981
0.7797 Intermediate Similarity NPC261506
0.7797 Intermediate Similarity NPC4328
0.7692 Intermediate Similarity NPC41061
0.7692 Intermediate Similarity NPC227551
0.7636 Intermediate Similarity NPC295823
0.7636 Intermediate Similarity NPC174720
0.7636 Intermediate Similarity NPC475467
0.7607 Intermediate Similarity NPC110633
0.7339 Intermediate Similarity NPC63159
0.7273 Intermediate Similarity NPC202828
0.7273 Intermediate Similarity NPC119592
0.7213 Intermediate Similarity NPC298034
0.7213 Intermediate Similarity NPC71065
0.719 Intermediate Similarity NPC43550
0.7182 Intermediate Similarity NPC148417
0.7177 Intermediate Similarity NPC250247
0.7107 Intermediate Similarity NPC258617
0.7105 Intermediate Similarity NPC473826
0.7064 Intermediate Similarity NPC112352
0.7059 Intermediate Similarity NPC488560
0.7034 Intermediate Similarity NPC309907
0.7018 Intermediate Similarity NPC241909
0.7009 Intermediate Similarity NPC79643
0.6992 Remote Similarity NPC136768
0.6891 Remote Similarity NPC155410
0.6833 Remote Similarity NPC475160
0.6833 Remote Similarity NPC100639
0.6833 Remote Similarity NPC473714
0.6825 Remote Similarity NPC220160
0.675 Remote Similarity NPC123199
0.6721 Remote Similarity NPC481080
0.6696 Remote Similarity NPC104071
0.6667 Remote Similarity NPC469776
0.664 Remote Similarity NPC65105
0.6639 Remote Similarity NPC475287
0.6637 Remote Similarity NPC102439
0.6549 Remote Similarity NPC160415
0.6532 Remote Similarity NPC476068
0.6532 Remote Similarity NPC57484
0.6491 Remote Similarity NPC480475
0.6446 Remote Similarity NPC192600
0.6414 Remote Similarity NPC32723
0.637 Remote Similarity NPC481323
0.637 Remote Similarity NPC469778
0.6364 Remote Similarity NPC48499
0.6356 Remote Similarity NPC481079
0.6348 Remote Similarity NPC101744
0.6341 Remote Similarity NPC475209
0.6328 Remote Similarity NPC481081
0.6308 Remote Similarity NPC224381
0.6284 Remote Similarity NPC135334
0.625 Remote Similarity NPC293330
0.625 Remote Similarity NPC161717
0.625 Remote Similarity NPC481078
0.6242 Remote Similarity NPC481324
0.6207 Remote Similarity NPC469775
0.6207 Remote Similarity NPC46665
0.6148 Remote Similarity NPC114287
0.6087 Remote Similarity NPC161674
0.6078 Remote Similarity NPC295941
0.605 Remote Similarity NPC134835
0.6033 Remote Similarity NPC480473
0.5985 Remote Similarity NPC70809
0.5973 Remote Similarity NPC469774
0.5948 Remote Similarity NPC469946
0.5906 Remote Similarity NPC470218
0.5902 Remote Similarity NPC480474
0.5882 Remote Similarity NPC480422
0.5868 Remote Similarity NPC73318
0.5855 Remote Similarity NPC100925
0.584 Remote Similarity NPC268184
0.5798 Remote Similarity NPC173859
0.5798 Remote Similarity NPC148603
0.5779 Remote Similarity NPC469777
0.575 Remote Similarity NPC68175
0.5726 Remote Similarity NPC295371
0.5702 Remote Similarity NPC297263
0.5682 Remote Similarity NPC475514
0.5669 Remote Similarity NPC469772
0.5656 Remote Similarity NPC601659
0.5641 Remote Similarity NPC473373
0.5625 Remote Similarity NPC128925
0.5614 Remote Similarity NPC90856
0.5606 Remote Similarity NPC286457
0.56 Remote Similarity NPC31838
0.56 Remote Similarity NPC36831
0.56 Remote Similarity NPC187290
0.5597 Remote Similarity NPC469773
0.5583 Remote Similarity NPC309714
0.5574 Remote Similarity NPC222580
0.5565 Remote Similarity NPC301449
0.5565 Remote Similarity NPC601290
0.5556 Remote Similarity NPC235405
0.5538 Remote Similarity NPC471550
0.5537 Remote Similarity NPC251768
0.5537 Remote Similarity NPC164389
0.5528 Remote Similarity NPC469821
0.5517 Remote Similarity NPC472268
0.5508 Remote Similarity NPC249848
0.5508 Remote Similarity NPC107966
0.5507 Remote Similarity NPC102505
0.5507 Remote Similarity NPC488514
0.5492 Remote Similarity NPC475591
0.5492 Remote Similarity NPC236870
0.5492 Remote Similarity NPC235438
0.5462 Remote Similarity NPC470512
0.5462 Remote Similarity NPC251263
0.5462 Remote Similarity NPC480419
0.5448 Remote Similarity NPC297950
0.5447 Remote Similarity NPC475504
0.5442 Remote Similarity NPC45606
0.5433 Remote Similarity NPC470915
0.5431 Remote Similarity NPC78046
0.5431 Remote Similarity NPC29069
0.541 Remote Similarity NPC10607
0.541 Remote Similarity NPC488526
0.541 Remote Similarity NPC232237
0.5397 Remote Similarity NPC80986
0.5373 Remote Similarity NPC480418
0.5373 Remote Similarity NPC13998
0.5372 Remote Similarity NPC192791
0.5366 Remote Similarity NPC105800
0.5354 Remote Similarity NPC104137
0.5354 Remote Similarity NPC26626
0.5344 Remote Similarity NPC219180
0.5333 Remote Similarity NPC470876
0.5328 Remote Similarity NPC309223
0.5328 Remote Similarity NPC30735
0.5308 Remote Similarity NPC123522
0.5302 Remote Similarity NPC220838
0.5294 Remote Similarity NPC56713
0.5289 Remote Similarity NPC473343
0.5286 Remote Similarity NPC480417
0.5285 Remote Similarity NPC11551
0.5267 Remote Similarity NPC470911
0.5263 Remote Similarity NPC47995
0.5234 Remote Similarity NPC207738
0.5214 Remote Similarity NPC204458
0.5214 Remote Similarity NPC214484
0.5207 Remote Similarity NPC39211
0.52 Remote Similarity NPC31193
0.5188 Remote Similarity NPC283417
0.5188 Remote Similarity NPC200049
0.5185 Remote Similarity NPC21691
0.5167 Remote Similarity NPC475516
0.5164 Remote Similarity NPC263756
0.5161 Remote Similarity NPC472269
0.5149 Remote Similarity NPC54636
0.5147 Remote Similarity NPC473452
0.5137 Remote Similarity NPC489208
0.5118 Remote Similarity NPC114484
0.5086 Remote Similarity NPC256798
0.5079 Remote Similarity NPC470514
0.5079 Remote Similarity NPC470513
0.5078 Remote Similarity NPC486564
0.5041 Remote Similarity NPC76497
0.5041 Remote Similarity NPC213674
0.504 Remote Similarity NPC104400
0.504 Remote Similarity NPC10320
0.5039 Remote Similarity NPC187618
0.5039 Remote Similarity NPC486563
0.5038 Remote Similarity NPC133818
0.5038 Remote Similarity NPC185466

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC165204 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