Natural Product: NPC185238

Natural Product IDNPC185238
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
SHDCOAGAKQAHTD-QDZUSAFCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 102317031
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 SHDCOAGAKQAHTD-QDZUSAFCSA-N
Standard InCHI InChI=1S/C60H96O30/c1-55(2)13-15-60(16-14-57(4)23(24(60)17-55)7-8-30-56(3)11-10-32(65)59(6,31(56)9-12-58(30,57)5)53(79)89-50-44(77)40(73)35(68)27(20-63)84-50)54(80)90-51-45(78)46(87-48-42(75)38(71)33(66)25(18-61)82-48)37(70)29(86-51)22-81-52-47(41(74)36(69)28(21-64)85-52)88-49-43(76)39(72)34(67)26(19-62)83-49/h7,24-52,61-78H,8-22H2,1-6H3/t24-,25+,26+,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+,56+,57+,58+,59-,60-/m0/s1
SMILES CC1(C)CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@@H]([C@](C)([C@@H]5CC[C@@]34C)C(=O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)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)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O1)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)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
NPO829 Vaccaria hispanica Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO829 Vaccaria hispanica Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO829 Vaccaria hispanica Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6752 Melandryum firmum n.a. n.a. n.a. n.a. n.a. n.a. Database[TM-MC]
NPO829 Vaccaria hispanica Species Caryophyllaceae 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 NPC185238 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
0.8416 Intermediate Similarity NPC69811
0.7736 Intermediate Similarity NPC75287
0.7647 Intermediate Similarity NPC473459
0.75 Intermediate Similarity NPC476992
0.7476 Intermediate Similarity NPC305267
0.7168 Intermediate Similarity NPC191827
0.6975 Remote Similarity NPC476991
0.6931 Remote Similarity NPC29069
0.6903 Remote Similarity NPC79643
0.6852 Remote Similarity NPC609763
0.6842 Remote Similarity NPC167383
0.6827 Remote Similarity NPC150400
0.6701 Remote Similarity NPC237503
0.6667 Remote Similarity NPC65105
0.6667 Remote Similarity NPC43550
0.6638 Remote Similarity NPC123199
0.6636 Remote Similarity NPC223301
0.6636 Remote Similarity NPC171544
0.6612 Remote Similarity NPC135849
0.6606 Remote Similarity NPC63159
0.6574 Remote Similarity NPC309714
0.6549 Remote Similarity NPC481078
0.6542 Remote Similarity NPC469946
0.6538 Remote Similarity NPC48499
0.6529 Remote Similarity NPC293330
0.6446 Remote Similarity NPC41061
0.6446 Remote Similarity NPC227551
0.6429 Remote Similarity NPC104372
0.6415 Remote Similarity NPC475516
0.64 Remote Similarity NPC250247
0.6396 Remote Similarity NPC475504
0.6341 Remote Similarity NPC305981
0.633 Remote Similarity NPC112352
0.629 Remote Similarity NPC261506
0.629 Remote Similarity NPC298034
0.629 Remote Similarity NPC71065
0.629 Remote Similarity NPC4328
0.625 Remote Similarity NPC25663
0.6147 Remote Similarity NPC295371
0.6126 Remote Similarity NPC104071
0.6106 Remote Similarity NPC222580
0.6071 Remote Similarity NPC102439
0.6071 Remote Similarity NPC480475
0.6066 Remote Similarity NPC481080
0.6016 Remote Similarity NPC476068
0.5984 Remote Similarity NPC70809
0.5966 Remote Similarity NPC475287
0.5965 Remote Similarity NPC297263
0.5952 Remote Similarity NPC202828
0.5952 Remote Similarity NPC119592
0.5952 Remote Similarity NPC236638
0.5952 Remote Similarity NPC294453
0.5952 Remote Similarity NPC481081
0.595 Remote Similarity NPC135904
0.5948 Remote Similarity NPC481079
0.5929 Remote Similarity NPC251768
0.5929 Remote Similarity NPC159309
0.5929 Remote Similarity NPC86222
0.5902 Remote Similarity NPC475160
0.5902 Remote Similarity NPC470218
0.5902 Remote Similarity NPC473714
0.5893 Remote Similarity NPC192791
0.5888 Remote Similarity NPC214484
0.5825 Remote Similarity NPC306746
0.5814 Remote Similarity NPC51564
0.5772 Remote Similarity NPC471550
0.5766 Remote Similarity NPC473373
0.5726 Remote Similarity NPC114484
0.5714 Remote Similarity NPC31838
0.5714 Remote Similarity NPC39211
0.5702 Remote Similarity NPC60557
0.5702 Remote Similarity NPC76972
0.5702 Remote Similarity NPC469782
0.5702 Remote Similarity NPC30735
0.5702 Remote Similarity NPC67857
0.5702 Remote Similarity NPC204414
0.5701 Remote Similarity NPC209894
0.5678 Remote Similarity NPC301449
0.5678 Remote Similarity NPC601290
0.5676 Remote Similarity NPC235405
0.5664 Remote Similarity NPC473343
0.5652 Remote Similarity NPC10607
0.5652 Remote Similarity NPC46665
0.5625 Remote Similarity NPC249848
0.5625 Remote Similarity NPC107966
0.5619 Remote Similarity NPC604133
0.5547 Remote Similarity NPC258617
0.5524 Remote Similarity NPC199457
0.552 Remote Similarity NPC100639
0.55 Remote Similarity NPC96641
0.55 Remote Similarity NPC163183
0.55 Remote Similarity NPC80986
0.549 Remote Similarity NPC191763
0.5481 Remote Similarity NPC46388
0.5476 Remote Similarity NPC488560
0.5472 Remote Similarity NPC68419
0.547 Remote Similarity NPC475591
0.547 Remote Similarity NPC236870
0.547 Remote Similarity NPC235438
0.5462 Remote Similarity NPC136768
0.5455 Remote Similarity NPC220160
0.5439 Remote Similarity NPC473884
0.5439 Remote Similarity NPC157868
0.5431 Remote Similarity NPC109588
0.5403 Remote Similarity NPC192600
0.5385 Remote Similarity NPC40775
0.5377 Remote Similarity NPC37739
0.5372 Remote Similarity NPC295823
0.5372 Remote Similarity NPC174720
0.5372 Remote Similarity NPC481030
0.5372 Remote Similarity NPC480473
0.5372 Remote Similarity NPC241909
0.5372 Remote Similarity NPC475467
0.5372 Remote Similarity NPC480474
0.5345 Remote Similarity NPC242840
0.5333 Remote Similarity NPC281148
0.5328 Remote Similarity NPC187290
0.5327 Remote Similarity NPC137917
0.5323 Remote Similarity NPC610204
0.5317 Remote Similarity NPC155410
0.5315 Remote Similarity NPC90856
0.5298 Remote Similarity NPC469778
0.5263 Remote Similarity NPC139894
0.5255 Remote Similarity NPC33012
0.5224 Remote Similarity NPC224381
0.5217 Remote Similarity NPC58448
0.52 Remote Similarity NPC300419
0.5191 Remote Similarity NPC475514
0.5182 Remote Similarity NPC8524
0.5169 Remote Similarity NPC160415
0.5167 Remote Similarity NPC123796
0.5159 Remote Similarity NPC469772
0.5159 Remote Similarity NPC295941
0.5154 Remote Similarity NPC57484
0.5126 Remote Similarity NPC148603
0.5124 Remote Similarity NPC471435
0.5124 Remote Similarity NPC471434
0.5118 Remote Similarity NPC323341
0.5118 Remote Similarity NPC470911
0.5118 Remote Similarity NPC481031
0.5115 Remote Similarity NPC110633
0.5088 Remote Similarity NPC475208
0.5086 Remote Similarity NPC173583
0.5078 Remote Similarity NPC166422
0.5064 Remote Similarity NPC469777
0.5043 Remote Similarity NPC470512
0.5038 Remote Similarity NPC21691
0.5036 Remote Similarity NPC477464

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC185238 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