Natural Product: NPC483415

Natural Product IDNPC483415
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
DMFHHIKBBFOXCL-CCTOFLRKSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10327084
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003533] Flavonoid-7-O-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 DMFHHIKBBFOXCL-CCTOFLRKSA-N
Standard InCHI InChI=1S/C30H34O17/c1-9-18(34)21(37)23(39)29(42-9)46-16-8-15-17(19(35)27(16)41-4)20(36)28(26(45-15)12-5-6-13(32)14(33)7-12)47-30-24(40)22(38)25(10(2)43-30)44-11(3)31/h5-10,18,21-25,29-30,32-35,37-40H,1-4H3/t9-,10-,18-,21+,22-,23+,24+,25-,29-,30-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)Oc1cc2c(c(c1OC)O)c(=O)c(c(c1ccc(c(c1)O)O)o2)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)OC(=O)C)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
NPO9114 Kalanchoe brasiliensis Species Crassulaceae Eukaryota n.a. n.a. n.a. PMID[16724848]
NPO9114 Kalanchoe brasiliensis Species Crassulaceae Eukaryota n.a. n.a. n.a. PMID[7853000]
NPO9114 Kalanchoe brasiliensis Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 10.0 ug.mL-1 PMID[7853000]

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 NPC483415 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
0.8506 High Similarity NPC483413
0.8295 Intermediate Similarity NPC483412
0.8276 Intermediate Similarity NPC483416
0.8125 Intermediate Similarity NPC27640
0.7955 Intermediate Similarity NPC483414
0.7294 Intermediate Similarity NPC488071
0.686 Remote Similarity NPC305811
0.686 Remote Similarity NPC271692
0.6633 Remote Similarity NPC470446
0.6413 Remote Similarity NPC265115
0.6404 Remote Similarity NPC59534
0.6263 Remote Similarity NPC473073
0.625 Remote Similarity NPC127546
0.625 Remote Similarity NPC57625
0.625 Remote Similarity NPC173637
0.625 Remote Similarity NPC317489
0.625 Remote Similarity NPC223424
0.625 Remote Similarity NPC600591
0.6196 Remote Similarity NPC605784
0.6154 Remote Similarity NPC159579
0.6129 Remote Similarity NPC488072
0.6117 Remote Similarity NPC470451
0.6111 Remote Similarity NPC46420
0.6111 Remote Similarity NPC24043
0.6087 Remote Similarity NPC21666
0.604 Remote Similarity NPC470445
0.602 Remote Similarity NPC126784
0.602 Remote Similarity NPC241423
0.6 Remote Similarity NPC158674
0.5978 Remote Similarity NPC182121
0.5978 Remote Similarity NPC611303
0.596 Remote Similarity NPC470443
0.5938 Remote Similarity NPC480466
0.59 Remote Similarity NPC606657
0.5889 Remote Similarity NPC249281
0.5882 Remote Similarity NPC470449
0.587 Remote Similarity NPC42773
0.587 Remote Similarity NPC45522
0.5851 Remote Similarity NPC209023
0.5806 Remote Similarity NPC175107
0.5784 Remote Similarity NPC471669
0.5766 Remote Similarity NPC488078
0.5714 Remote Similarity NPC471748
0.5699 Remote Similarity NPC117260
0.5699 Remote Similarity NPC201292
0.5657 Remote Similarity NPC233994
0.5657 Remote Similarity NPC605592
0.5652 Remote Similarity NPC136042
0.5638 Remote Similarity NPC219904
0.5625 Remote Similarity NPC276377
0.5625 Remote Similarity NPC355481
0.5604 Remote Similarity NPC111929
0.5604 Remote Similarity NPC320283
0.5604 Remote Similarity NPC41121
0.5591 Remote Similarity NPC84362
0.5591 Remote Similarity NPC349108
0.5591 Remote Similarity NPC603655
0.5567 Remote Similarity NPC116864
0.5567 Remote Similarity NPC244776
0.5556 Remote Similarity NPC18772
0.5534 Remote Similarity NPC64755
0.5532 Remote Similarity NPC599850
0.5521 Remote Similarity NPC223747
0.5521 Remote Similarity NPC116458
0.5521 Remote Similarity NPC246943
0.551 Remote Similarity NPC254540
0.55 Remote Similarity NPC203259
0.55 Remote Similarity NPC33054
0.55 Remote Similarity NPC176740
0.55 Remote Similarity NPC471725
0.55 Remote Similarity NPC134532
0.55 Remote Similarity NPC602582
0.549 Remote Similarity NPC75574
0.549 Remote Similarity NPC211532
0.549 Remote Similarity NPC488364
0.5481 Remote Similarity NPC473071
0.5437 Remote Similarity NPC72016
0.5435 Remote Similarity NPC135599
0.5435 Remote Similarity NPC73855
0.5435 Remote Similarity NPC113968
0.5435 Remote Similarity NPC328940
0.5435 Remote Similarity NPC277174
0.5435 Remote Similarity NPC606877
0.5392 Remote Similarity NPC488073
0.5392 Remote Similarity NPC488074
0.5354 Remote Similarity NPC251417
0.5347 Remote Similarity NPC150164
0.5333 Remote Similarity NPC470447
0.5327 Remote Similarity NPC470455
0.5319 Remote Similarity NPC145038
0.5319 Remote Similarity NPC56077
0.5319 Remote Similarity NPC281131
0.5319 Remote Similarity NPC253662
0.5319 Remote Similarity NPC265530
0.5319 Remote Similarity NPC179950
0.5319 Remote Similarity NPC88789
0.5319 Remote Similarity NPC491374
0.5294 Remote Similarity NPC473571
0.5294 Remote Similarity NPC110941
0.5294 Remote Similarity NPC186816
0.5263 Remote Similarity NPC45638
0.5238 Remote Similarity NPC486577
0.5213 Remote Similarity NPC19709
0.5213 Remote Similarity NPC238376
0.52 Remote Similarity NPC480463
0.5185 Remote Similarity NPC14187
0.5161 Remote Similarity NPC67037
0.5161 Remote Similarity NPC255615
0.5149 Remote Similarity NPC29958
0.5149 Remote Similarity NPC139320
0.5146 Remote Similarity NPC204693
0.5143 Remote Similarity NPC104883
0.5143 Remote Similarity NPC488679
0.513 Remote Similarity NPC156785
0.5104 Remote Similarity NPC52550
0.5104 Remote Similarity NPC105025
0.5104 Remote Similarity NPC488080
0.5104 Remote Similarity NPC169977
0.51 Remote Similarity NPC211594
0.5086 Remote Similarity NPC488079
0.5053 Remote Similarity NPC289667
0.505 Remote Similarity NPC473682
0.5047 Remote Similarity NPC89127

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC483415 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
0.55 Remote Similarity NPD6797 Phase 2
0.5481 Remote Similarity NPD7251 Phase 2

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