Natural Product: NPC815

Natural Product IDNPC815
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
HCKUIVZXCXTBEH-PSRBGVDOSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 70698266
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 HCKUIVZXCXTBEH-PSRBGVDOSA-N
Standard InCHI InChI=1S/C52H84O24/c1-21-39(73-42-36(65)31(60)25(57)17-69-42)35(64)38(67)43(71-21)74-40-32(61)26(58)18-70-45(40)76-46(68)52-12-11-47(2,3)13-23(52)22-7-8-28-48(4)14-24(56)41(75-44-37(66)34(63)33(62)27(16-53)72-44)51(19-54,20-55)29(48)9-10-49(28,5)50(22,6)15-30(52)59/h7,21,23-45,53-67H,8-20H2,1-6H3/t21-,23-,24-,25+,26-,27+,28+,29+,30+,31-,32-,33+,34-,35-,36+,37+,38+,39-,40+,41-,42-,43-,44-,45-,48+,49+,50+,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]1OC(=O)[C@]12CCC(C)(C)C[C@H]1C1=CC[C@@H]3[C@@]4(C)C[C@@H]([C@@H](C(CO)(CO)[C@@H]4CC[C@@]3(C)[C@]1(C)C[C@H]2O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1092.54 Volume:   1036.632
?
Van der Waals volume.
Dense:   1.054 LogP:   -0.28
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.516
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.389
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   51.0
TPSA:   394.36
?
Topological Polar Surface Area.
H-Bond Acceptor:   24.0
H-Bond Donor:   15.0 Rings:   9.0
Heavy Atoms:   24.0

MedChem Properties

QED Drug-Likeness Score:   0.054 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.009 Fsp3:   0.942
MCE-18:   198.238
?
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:   0.68 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.007
?
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:   0.199 Promiscuous compounds:   0.122

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.218 MDCK Permeability:   -5.01
Pgp-inhibitor:   0.0 Pgp-substrate:   0.99
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):   0.981
20% Bioavailability (F20%):   0.479 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.058 MRP1:   0.035
Plasma Protein Binding (PPB):   53.163% Volume Distribution (VD):   -0.392
Fu: 29.221%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.006
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:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.063
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):  -0.457 Half-life (T1/2):  3.82

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.002
Human Hepatotoxicity (H-HT):  0.714 Drug-induced Liver Injury (DILI):  0.716
AMES Toxicity:  0.937 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.049 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.723 Drug-induced Nephrotoxicity:  0.998
Genotoxicity:  0.022 RPMI-8226 Immunitoxicity:  0.299
A549 Cytotoxicity:  0.817 Hek293 Cytotoxicity:  0.207
BCF:   0.986
?
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:   3.371
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.953
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.841
?
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
NPO29808 Platycodon grandiflorum Species Campanulaceae Eukaryota n.a. root n.a. PMID[17851435]
NPO29808 Platycodon grandiflorum Species Campanulaceae Eukaryota Roots n.a. n.a. PMID[20939516]
NPO29808 Platycodon grandiflorum Species Campanulaceae Eukaryota n.a. root n.a. PMID[20939516]
NPO29808 Platycodon grandiflorum Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29808 Platycodon grandiflorum Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO214 Platycodon grandiflorus Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29808 Platycodon grandiflorum Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO214 Platycodon grandiflorus Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO214 Platycodon grandiflorus Species Campanulaceae 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
NPT28438 Unchecked Unchecked n.a. IC50 = 8240.0 nM PMID[29353722]

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 NPC815 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
0.8393 Intermediate Similarity NPC37860
0.8365 Intermediate Similarity NPC104137
0.8365 Intermediate Similarity NPC26626
0.8103 Intermediate Similarity NPC293031
0.7759 Intermediate Similarity NPC144644
0.7759 Intermediate Similarity NPC170407
0.7719 Intermediate Similarity NPC473452
0.7699 Intermediate Similarity NPC85154
0.7565 Intermediate Similarity NPC286457
0.75 Intermediate Similarity NPC68767
0.7479 Intermediate Similarity NPC267694
0.7438 Intermediate Similarity NPC110385
0.7368 Intermediate Similarity NPC480423
0.7179 Intermediate Similarity NPC237191
0.7037 Intermediate Similarity NPC164389
0.6917 Remote Similarity NPC470876
0.6911 Remote Similarity NPC142151
0.688 Remote Similarity NPC153673
0.6833 Remote Similarity NPC13998
0.6746 Remote Similarity NPC51099
0.6719 Remote Similarity NPC275225
0.6614 Remote Similarity NPC489209
0.6604 Remote Similarity NPC475208
0.6509 Remote Similarity NPC1046
0.65 Remote Similarity NPC283417
0.65 Remote Similarity NPC200049
0.6475 Remote Similarity NPC57484
0.6422 Remote Similarity NPC480420
0.6417 Remote Similarity NPC480419
0.6387 Remote Similarity NPC123522
0.6316 Remote Similarity NPC489208
0.6279 Remote Similarity NPC102505
0.6279 Remote Similarity NPC488514
0.626 Remote Similarity NPC33012
0.6212 Remote Similarity NPC480421
0.6183 Remote Similarity NPC8524
0.6174 Remote Similarity NPC488517
0.617 Remote Similarity NPC485563
0.614 Remote Similarity NPC488526
0.6136 Remote Similarity NPC485562
0.6129 Remote Similarity NPC4749
0.6124 Remote Similarity NPC220160
0.6094 Remote Similarity NPC309223
0.608 Remote Similarity NPC473386
0.6048 Remote Similarity NPC471577
0.6032 Remote Similarity NPC480418
0.5923 Remote Similarity NPC70809
0.5902 Remote Similarity NPC300419
0.5862 Remote Similarity NPC305267
0.5859 Remote Similarity NPC471580
0.5847 Remote Similarity NPC64715
0.5827 Remote Similarity NPC21691
0.5818 Remote Similarity NPC238935
0.5806 Remote Similarity NPC475899
0.5776 Remote Similarity NPC117714
0.5725 Remote Similarity NPC302543
0.5641 Remote Similarity NPC30289
0.5614 Remote Similarity NPC139894
0.561 Remote Similarity NPC11242
0.5603 Remote Similarity NPC263756
0.5603 Remote Similarity NPC469946
0.5575 Remote Similarity NPC179434
0.5574 Remote Similarity NPC69811
0.5556 Remote Similarity NPC112352
0.5546 Remote Similarity NPC63159
0.5541 Remote Similarity NPC23020
0.5528 Remote Similarity NPC481078
0.5522 Remote Similarity NPC478823
0.5522 Remote Similarity NPC482010
0.5512 Remote Similarity NPC135904
0.5492 Remote Similarity NPC481079
0.547 Remote Similarity NPC213674
0.5462 Remote Similarity NPC232237
0.5433 Remote Similarity NPC284449
0.5431 Remote Similarity NPC150400
0.543 Remote Similarity NPC472270
0.543 Remote Similarity NPC112492
0.542 Remote Similarity NPC265841
0.5407 Remote Similarity NPC224381
0.5403 Remote Similarity NPC207738
0.5397 Remote Similarity NPC475287
0.5397 Remote Similarity NPC76972
0.5397 Remote Similarity NPC469782
0.5397 Remote Similarity NPC204414
0.5385 Remote Similarity NPC295371
0.538 Remote Similarity NPC488513
0.5372 Remote Similarity NPC475504
0.5372 Remote Similarity NPC297263
0.5347 Remote Similarity NPC329893
0.5344 Remote Similarity NPC484943
0.5338 Remote Similarity NPC476779
0.5328 Remote Similarity NPC480417
0.5303 Remote Similarity NPC476774
0.5299 Remote Similarity NPC202828
0.5299 Remote Similarity NPC119592
0.528 Remote Similarity NPC31838
0.528 Remote Similarity NPC187290
0.5276 Remote Similarity NPC60557
0.5276 Remote Similarity NPC67857
0.5273 Remote Similarity NPC48249
0.5271 Remote Similarity NPC257211
0.5271 Remote Similarity NPC123199
0.5263 Remote Similarity NPC41061
0.5263 Remote Similarity NPC227551
0.5263 Remote Similarity NPC475514
0.5259 Remote Similarity NPC298034
0.5259 Remote Similarity NPC71065
0.5242 Remote Similarity NPC301449
0.5242 Remote Similarity NPC601290
0.5224 Remote Similarity NPC293330
0.5221 Remote Similarity NPC476775
0.521 Remote Similarity NPC473343
0.521 Remote Similarity NPC76497
0.52 Remote Similarity NPC241909
0.5191 Remote Similarity NPC25663
0.5188 Remote Similarity NPC488308
0.5188 Remote Similarity NPC476780
0.5185 Remote Similarity NPC236638
0.5185 Remote Similarity NPC294453
0.5185 Remote Similarity NPC305981
0.5149 Remote Similarity NPC271610
0.5149 Remote Similarity NPC312650
0.5147 Remote Similarity NPC261506
0.5147 Remote Similarity NPC4328
0.5137 Remote Similarity NPC472268
0.5116 Remote Similarity NPC79643
0.5108 Remote Similarity NPC476776
0.5091 Remote Similarity NPC237503
0.5086 Remote Similarity NPC29069
0.5083 Remote Similarity NPC80843
0.5079 Remote Similarity NPC295823
0.5079 Remote Similarity NPC174720
0.5079 Remote Similarity NPC475467
0.5078 Remote Similarity NPC185466
0.5078 Remote Similarity NPC288205
0.5078 Remote Similarity NPC51465
0.5074 Remote Similarity NPC110700
0.5074 Remote Similarity NPC481081
0.5074 Remote Similarity NPC476777
0.5069 Remote Similarity NPC475177
0.5068 Remote Similarity NPC484831
0.5068 Remote Similarity NPC297950
0.5068 Remote Similarity NPC475394
0.5068 Remote Similarity NPC484830
0.5064 Remote Similarity NPC322904
0.5041 Remote Similarity NPC105800
0.5039 Remote Similarity NPC610204
0.5038 Remote Similarity NPC475209
0.5038 Remote Similarity NPC481080
0.5038 Remote Similarity NPC603137
0.5036 Remote Similarity NPC250247
0.5036 Remote Similarity NPC279915
0.5036 Remote Similarity NPC476778
0.5033 Remote Similarity NPC488619

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC815 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