Natural Product: NPC488625

Natural Product IDNPC488625
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 LDNNXGDTUTXATF-PGDVHREDSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44584145
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002518] Annonaceous acetogenins

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 LDNNXGDTUTXATF-PGDVHREDSA-N
Standard InCHI InChI=1S/C38H68O8/c1-5-6-7-8-9-10-11-12-13-17-20-33(40)35-23-24-36(44-35)34(41)22-21-32-27-31(45-38(3,4)46-32)19-16-14-15-18-30(39)26-29-25-28(2)43-37(29)42/h25,28,30-36,39-41H,5-24,26-27H2,1-4H3/t28-,30+,31+,32-,33+,34+,35+,36+/m0/s1
SMILES CCCCCCCCCCCC[C@H]([C@H]1CC[C@H]([C@@H](CC[C@H]2C[C@@H](CCCCC[C@H](CC3=C[C@H](C)OC3=O)O)OC(C)(C)O2)O)O1)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
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11473425]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11975482]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. stem n.a. PMID[17401878]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. leaf n.a. PMID[17401878]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. root n.a. PMID[17401878]
NPO26234 Annona muricata Species Annonaceae Eukaryota Leaves n.a. n.a. PMID[7494150]
NPO26234 Annona muricata Species Annonaceae Eukaryota Leaves n.a. n.a. PMID[7673926]
NPO26234 Annona muricata Species Annonaceae Eukaryota Leaves n.a. n.a. PMID[7673935]
NPO26234 Annona muricata Species Annonaceae Eukaryota Leaves n.a. n.a. PMID[7673936]
NPO26234 Annona muricata Species Annonaceae Eukaryota leaves n.a. n.a. PMID[8946744]
NPO26234 Annona muricata Species Annonaceae Eukaryota seeds n.a. n.a. PMID[8991944]
NPO26234 Annona muricata Species Annonaceae Eukaryota Leaves n.a. n.a. PMID[9584396]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26234 Annona muricata Species Annonaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26234 Annona muricata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26234 Annona muricata Species Annonaceae 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
NPT81 Cell line A549 Homo sapiens ED50 = 3.67 10'-3 ug/ml PMID[7673935]
NPT83 Cell line MCF7 Homo sapiens ED50 = 1.65 10'-1 ug/ml PMID[7673935]
NPT139 Cell line HT-29 Homo sapiens ED50 = 5.08 10'-1 ug/ml PMID[7673935]

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
- Artemia LC50 = 0.206 ug.mL-1 PMID[7673935]

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 NPC488625 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
1.0 High Similarity NPC488630
1.0 High Similarity NPC488626
0.7857 Intermediate Similarity NPC488623
0.7857 Intermediate Similarity NPC488624
0.7857 Intermediate Similarity NPC488629
0.7647 Intermediate Similarity NPC606043
0.7636 Intermediate Similarity NPC20621
0.7636 Intermediate Similarity NPC318963
0.7636 Intermediate Similarity NPC605101
0.7547 Intermediate Similarity NPC182383
0.75 Intermediate Similarity NPC107986
0.75 Intermediate Similarity NPC223871
0.75 Intermediate Similarity NPC231009
0.75 Intermediate Similarity NPC103284
0.75 Intermediate Similarity NPC110710
0.75 Intermediate Similarity NPC1083
0.75 Intermediate Similarity NPC82795
0.75 Intermediate Similarity NPC286338
0.75 Intermediate Similarity NPC603931
0.75 Intermediate Similarity NPC604237
0.7358 Intermediate Similarity NPC488253
0.7358 Intermediate Similarity NPC473669
0.7358 Intermediate Similarity NPC488251
0.7222 Intermediate Similarity NPC232555
0.7222 Intermediate Similarity NPC171174
0.7222 Intermediate Similarity NPC114694
0.7222 Intermediate Similarity NPC485248
0.7222 Intermediate Similarity NPC142117
0.7222 Intermediate Similarity NPC480249
0.7222 Intermediate Similarity NPC485249
0.7222 Intermediate Similarity NPC240695
0.7193 Intermediate Similarity NPC473478
0.7193 Intermediate Similarity NPC473651
0.7193 Intermediate Similarity NPC66346
0.7091 Intermediate Similarity NPC488632
0.7091 Intermediate Similarity NPC134865
0.7091 Intermediate Similarity NPC103523
0.7091 Intermediate Similarity NPC488627
0.7091 Intermediate Similarity NPC47937
0.7091 Intermediate Similarity NPC488631
0.7069 Intermediate Similarity NPC283085
0.7069 Intermediate Similarity NPC169511
0.7069 Intermediate Similarity NPC287164
0.7069 Intermediate Similarity NPC234077
0.7018 Intermediate Similarity NPC602738
0.6964 Remote Similarity NPC280621
0.6964 Remote Similarity NPC48338
0.6964 Remote Similarity NPC488628
0.6909 Remote Similarity NPC81045
0.6909 Remote Similarity NPC39754
0.6909 Remote Similarity NPC171135
0.6909 Remote Similarity NPC61257
0.6909 Remote Similarity NPC320569
0.6909 Remote Similarity NPC133730
0.6909 Remote Similarity NPC191929
0.6909 Remote Similarity NPC100454
0.6909 Remote Similarity NPC242364
0.6909 Remote Similarity NPC172821
0.6909 Remote Similarity NPC274446
0.6909 Remote Similarity NPC485251
0.6909 Remote Similarity NPC151403
0.6909 Remote Similarity NPC261952
0.6909 Remote Similarity NPC605171
0.6842 Remote Similarity NPC178215
0.6842 Remote Similarity NPC473687
0.6842 Remote Similarity NPC204686
0.6842 Remote Similarity NPC219498
0.6842 Remote Similarity NPC308412
0.6842 Remote Similarity NPC134885
0.6842 Remote Similarity NPC488247
0.6842 Remote Similarity NPC210218
0.6842 Remote Similarity NPC488248
0.6786 Remote Similarity NPC93794
0.6786 Remote Similarity NPC473504
0.6786 Remote Similarity NPC81778
0.6786 Remote Similarity NPC40066
0.678 Remote Similarity NPC231096
0.678 Remote Similarity NPC475581
0.678 Remote Similarity NPC62118
0.678 Remote Similarity NPC132496
0.678 Remote Similarity NPC107717
0.678 Remote Similarity NPC488252
0.6774 Remote Similarity NPC473663
0.6774 Remote Similarity NPC473723
0.6774 Remote Similarity NPC475173
0.6724 Remote Similarity NPC488250
0.6721 Remote Similarity NPC91067
0.661 Remote Similarity NPC69082
0.661 Remote Similarity NPC488249
0.6552 Remote Similarity NPC42598
0.65 Remote Similarity NPC130359
0.65 Remote Similarity NPC14901
0.6491 Remote Similarity NPC477011
0.6452 Remote Similarity NPC480081
0.6441 Remote Similarity NPC134807
0.6308 Remote Similarity NPC482766
0.625 Remote Similarity NPC100921
0.625 Remote Similarity NPC475159
0.625 Remote Similarity NPC131002
0.625 Remote Similarity NPC473780
0.625 Remote Similarity NPC477018
0.625 Remote Similarity NPC604521
0.623 Remote Similarity NPC258068
0.623 Remote Similarity NPC476583
0.623 Remote Similarity NPC606740
0.623 Remote Similarity NPC608614
0.6182 Remote Similarity NPC112685
0.6154 Remote Similarity NPC608138
0.6129 Remote Similarity NPC233551
0.6129 Remote Similarity NPC40376
0.6129 Remote Similarity NPC21208
0.6129 Remote Similarity NPC477014
0.6129 Remote Similarity NPC477013
0.6102 Remote Similarity NPC241360
0.6102 Remote Similarity NPC293136
0.6061 Remote Similarity NPC279267
0.6034 Remote Similarity NPC156804
0.6032 Remote Similarity NPC239517
0.6 Remote Similarity NPC73310
0.6 Remote Similarity NPC473529
0.6 Remote Similarity NPC180363
0.6 Remote Similarity NPC94875
0.6 Remote Similarity NPC11332
0.6 Remote Similarity NPC145914
0.6 Remote Similarity NPC601174
0.6 Remote Similarity NPC601403
0.6 Remote Similarity NPC603568
0.6 Remote Similarity NPC604330
0.6 Remote Similarity NPC608300
0.6 Remote Similarity NPC611200
0.6 Remote Similarity NPC611571
0.5932 Remote Similarity NPC163093
0.5806 Remote Similarity NPC20339
0.5738 Remote Similarity NPC65930
0.569 Remote Similarity NPC329829
0.5667 Remote Similarity NPC473649
0.5667 Remote Similarity NPC473156
0.5667 Remote Similarity NPC154097
0.5667 Remote Similarity NPC159750
0.5667 Remote Similarity NPC73248
0.5667 Remote Similarity NPC282815
0.5667 Remote Similarity NPC470401
0.5667 Remote Similarity NPC600956
0.5667 Remote Similarity NPC610454
0.5645 Remote Similarity NPC309211
0.5645 Remote Similarity NPC329838
0.5645 Remote Similarity NPC477010
0.5588 Remote Similarity NPC477017
0.5588 Remote Similarity NPC477016
0.5574 Remote Similarity NPC473671
0.5574 Remote Similarity NPC475268
0.5574 Remote Similarity NPC470400
0.5574 Remote Similarity NPC77871
0.5574 Remote Similarity NPC9678
0.5574 Remote Similarity NPC319036
0.5574 Remote Similarity NPC604764
0.5574 Remote Similarity NPC605867
0.5484 Remote Similarity NPC132940
0.5469 Remote Similarity NPC473995
0.5441 Remote Similarity NPC488245
0.5424 Remote Similarity NPC25764
0.5424 Remote Similarity NPC235809
0.5424 Remote Similarity NPC39279
0.5424 Remote Similarity NPC39167
0.5424 Remote Similarity NPC292809
0.5424 Remote Similarity NPC202055
0.5424 Remote Similarity NPC606804
0.5424 Remote Similarity NPC607425
0.5424 Remote Similarity NPC608574
0.541 Remote Similarity NPC144415
0.541 Remote Similarity NPC607439
0.541 Remote Similarity NPC608157
0.5397 Remote Similarity NPC329615
0.5397 Remote Similarity NPC20533
0.5373 Remote Similarity NPC477015
0.5323 Remote Similarity NPC480079
0.5312 Remote Similarity NPC473707
0.5312 Remote Similarity NPC139418
0.5238 Remote Similarity NPC473904
0.5231 Remote Similarity NPC120398
0.5231 Remote Similarity NPC471567
0.5224 Remote Similarity NPC473520
0.5161 Remote Similarity NPC482767
0.5161 Remote Similarity NPC488246
0.5161 Remote Similarity NPC475260
0.5161 Remote Similarity NPC488621
0.5161 Remote Similarity NPC473775
0.5161 Remote Similarity NPC488622
0.5161 Remote Similarity NPC480080
0.5161 Remote Similarity NPC600524
0.5161 Remote Similarity NPC608355
0.5152 Remote Similarity NPC89001
0.5152 Remote Similarity NPC320458
0.5152 Remote Similarity NPC480082
0.5147 Remote Similarity NPC253801
0.5079 Remote Similarity NPC219652
0.5079 Remote Similarity NPC473840
0.5077 Remote Similarity NPC11456
0.5077 Remote Similarity NPC477012

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC488625 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