Natural Product: NPC479128

Natural Product IDNPC479128
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
DTHNMHAUYICORS-KTKZVXAJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 16133831
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0003297] Organic Polymers
      • [CHEMONTID:0003298] Polypeptides

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 DTHNMHAUYICORS-KTKZVXAJSA-N
Standard InCHI InChI=1S/C149H226N40O45/c1-17-76(10)119(146(232)167-80(14)126(212)175-104(60-86-63-159-91-36-25-24-35-89(86)91)136(222)177-100(56-73(4)5)137(223)186-117(74(6)7)144(230)174-93(37-26-28-52-150)128(214)160-65-110(197)168-92(122(154)208)39-30-54-158-149(155)156)188-138(224)102(57-83-31-20-18-21-32-83)178-133(219)98(47-51-115(204)205)173-132(218)94(38-27-29-53-151)170-124(210)78(12)164-123(209)77(11)166-131(217)97(44-48-109(153)196)169-111(198)66-161-130(216)96(46-50-114(202)203)172-134(220)99(55-72(2)3)176-135(221)101(59-85-40-42-88(195)43-41-85)179-141(227)106(68-190)182-143(229)108(70-192)183-145(231)118(75(8)9)187-140(226)105(62-116(206)207)180-142(228)107(69-191)184-148(234)121(82(16)194)189-139(225)103(58-84-33-22-19-23-34-84)181-147(233)120(81(15)193)185-112(199)67-162-129(215)95(45-49-113(200)201)171-125(211)79(13)165-127(213)90(152)61-87-64-157-71-163-87/h18-25,31-36,40-43,63-64,71-82,90,92-108,117-121,159,190-195H,17,26-30,37-39,44-62,65-70,150-152H2,1-16H3,(H2,153,196)(H2,154,208)(H,157,163)(H,160,214)(H,161,216)(H,162,215)(H,164,209)(H,165,213)(H,166,217)(H,167,232)(H,168,197)(H,169,198)(H,170,210)(H,171,211)(H,172,220)(H,173,218)(H,174,230)(H,175,212)(H,176,221)(H,177,222)(H,178,219)(H,179,227)(H,180,228)(H,181,233)(H,182,229)(H,183,231)(H,184,234)(H,185,199)(H,186,223)(H,187,226)(H,188,224)(H,189,225)(H,200,201)(H,202,203)(H,204,205)(H,206,207)(H4,155,156,158)/t76-,77-,78-,79-,80-,81+,82+,90-,92-,93-,94-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,107-,108-,117-,118-,119-,120-,121-/m0/s1
SMILES CC[C@H](C)[C@@H](C(=N[C@@H](C)C(=N[C@@H](Cc1c[nH]c2ccccc12)C(=N[C@@H](CC(C)C)C(=N[C@@H](C(C)C)C(=N[C@@H](CCCCN)C(=NCC(=N[C@@H](CCCNC(=N)N)C(=N)O)O)O)O)O)O)O)O)N=C([C@H](Cc1ccccc1)N=C([C@H](CCC(=O)O)N=C([C@H](CCCCN)N=C([C@H](C)N=C([C@H](C)N=C([C@H](CCC(=N)O)N=C(CN=C([C@H](CCC(=O)O)N=C([C@H](CC(C)C)N=C([C@H](Cc1ccc(cc1)O)N=C([C@H](CO)N=C([C@H](CO)N=C([C@H](C(C)C)N=C([C@H](CC(=O)O)N=C([C@H](CO)N=C([C@H]([C@@H](C)O)N=C([C@H](Cc1ccccc1)N=C([C@H]([C@@H](C)O)N=C(CN=C([C@H](CCC(=O)O)N=C([C@H](C)N=C([C@H](Cc1cnc[nH]1)N)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO40161 Hoplobatrachus occipitalis Species Dicroglossidae Eukaryota Skin Secretion n.a. n.a. PMID[27560386]

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
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens IC50 = 14.0 nM PMID[15357960]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 15.4 nM PMID[15357960]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens IC50 = 0.14 nM PMID[15357960]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 0.4 nM PMID[15357960]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens IC50 = 1.9 nM PMID[18950150]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 1.0 nM PMID[18950150]
NPT1592 Individual protein Dipeptidyl peptidase IV Homo sapiens Activity = 11.0 % PMID[18656368]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 0.35 nM PMID[24044354]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens IC50 = 1.5 nM PMID[24044354]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 0.0033 nM PMID[24308627]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 0.044 nM PMID[28771355]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 0.0009 nM PMID[28448133]
NPT1814 Individual protein Glucagon receptor Homo sapiens EC50 > 0.001 nM PMID[28448133]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 0.05012 nM PMID[29939744]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 3.981 nM PMID[29939744]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 7.943 nM PMID[29939744]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens Emax = 100.0 % PMID[37286364]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 131.0 nM PMID[37286364]
NPT1814 Individual protein Glucagon receptor Homo sapiens EC50 > 100.0 nM PMID[36571995]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens Activity n.a. n.a. n.a. PMID[35984914]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 0.003 nM PMID[37286364]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 97.0 nM PMID[37286364]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 0.006 nM PMID[35978682]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 25.12 nM PMID[35984914]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 0.057 nM PMID[36571995]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 794.33 nM PMID[35984914]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens IC50 = 7.943 nM PMID[35984914]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 0.001585 nM PMID[35984914]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 100.0 nM PMID[35984914]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 0.084 nM PMID[35231829]
NPT239 Individual protein Cholecystokinin A receptor Homo sapiens EC50 n.a. n.a. n.a. PMID[35231829]
NPT101 Individual protein Glucagon-like peptide 1 receptor Homo sapiens EC50 = 67.0 nM PMID[37286364]
NPT18191 Single protein Glucagon receptor Mus musculus EC50 > 10000.0 nM PMID[28448133]
NPT4729 Individual protein Cholecystokinin B receptor Homo sapiens EC50 n.a. n.a. n.a. PMID[35231829]
NPT18189 Single protein Glucagon-like peptide 1 receptor Mus musculus EC50 = 0.0009 nM PMID[28448133]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[35984914]
NPT28438 Unchecked Unchecked n.a. EC50 = 0.003 nM PMID[35978682]
NPT28438 Unchecked Unchecked n.a. Activity = 25.0 % PMID[35984914]
NPT2 Others Unspecified n.a. Activity = 3.3 ng PMID[26606380]
NPT2 Others Unspecified n.a. Activity = 3.14 ng PMID[27560386]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Activity = 17.12 mmol/L PMID[18656368]
NPT32 Organism Mus musculus Mus musculus Activity = 12.1 mmol/L PMID[18656368]
NPT32 Organism Mus musculus Mus musculus Activity = 8.08 mmol/L PMID[18656368]
NPT32 Organism Mus musculus Mus musculus Activity = 7.68 mmol/L PMID[18656368]
NPT32 Organism Mus musculus Mus musculus Activity = 23.27 mmol/L PMID[18656368]
NPT32 Organism Mus musculus Mus musculus Activity = 18.02 mmol/L PMID[18656368]
NPT32 Organism Mus musculus Mus musculus Activity = 13.48 mmol/L PMID[18656368]
NPT32 Organism Mus musculus Mus musculus Activity = 9.83 mmol/L PMID[18656368]
NPT32 Organism Mus musculus Mus musculus Activity = 30.0 % PMID[24044354]
NPT32 Organism Mus musculus Mus musculus Activity n.a. n.a. n.a. PMID[35984914]





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference
Cricetulus griseus n.a. Drug uptake n.a. n.a. n.a. PMID[35984914]





 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 NPC479128 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
0.8021 Intermediate Similarity NPC478504
0.6839 Remote Similarity NPC486513
0.6737 Remote Similarity NPC477634
0.6684 Remote Similarity NPC477633
0.6609 Remote Similarity NPC479136
0.6369 Remote Similarity NPC479133
0.6283 Remote Similarity NPC486506
0.6283 Remote Similarity NPC485247
0.6283 Remote Similarity NPC486514
0.6263 Remote Similarity NPC477635
0.623 Remote Similarity NPC489511
0.62 Remote Similarity NPC486517
0.6178 Remote Similarity NPC486515
0.6069 Remote Similarity NPC479132
0.6034 Remote Similarity NPC479135
0.6033 Remote Similarity NPC320968
0.6009 Remote Similarity NPC480594
0.6 Remote Similarity NPC479141
0.5972 Remote Similarity NPC480533
0.595 Remote Similarity NPC329843
0.5931 Remote Similarity NPC489512
0.5899 Remote Similarity NPC480595
0.5896 Remote Similarity NPC484882
0.5845 Remote Similarity NPC479082
0.5829 Remote Similarity NPC484347
0.5759 Remote Similarity NPC484964
0.5758 Remote Similarity NPC484880
0.5729 Remote Similarity NPC489217
0.5721 Remote Similarity NPC485244
0.5632 Remote Similarity NPC486505
0.5628 Remote Similarity NPC479130
0.5628 Remote Similarity NPC479129
0.5602 Remote Similarity NPC479872
0.5598 Remote Similarity NPC479083
0.558 Remote Similarity NPC479131
0.5579 Remote Similarity NPC484963
0.5579 Remote Similarity NPC486507
0.555 Remote Similarity NPC477632
0.55 Remote Similarity NPC485116
0.5497 Remote Similarity NPC485115
0.538 Remote Similarity NPC484883
0.5347 Remote Similarity NPC484965
0.5325 Remote Similarity NPC479134
0.5243 Remote Similarity NPC484874
0.5233 Remote Similarity NPC479121
0.5231 Remote Similarity NPC485246
0.5211 Remote Similarity NPC481409
0.5202 Remote Similarity NPC485243
0.5174 Remote Similarity NPC484363
0.5127 Remote Similarity NPC485245
0.5104 Remote Similarity NPC153400
0.5099 Remote Similarity NPC486503
0.5092 Remote Similarity NPC479572
0.5092 Remote Similarity NPC479568
0.5092 Remote Similarity NPC479573
0.5092 Remote Similarity NPC479566
0.5092 Remote Similarity NPC479567
0.5092 Remote Similarity NPC479569
0.5092 Remote Similarity NPC479571
0.5075 Remote Similarity NPC484365
0.5061 Remote Similarity NPC479570

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC479128 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
0.528 Remote Similarity NPD8458 Clinical (unspecified phase)

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