Natural Product: NPC275152

Natural Product IDNPC275152
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GMXMKSFJQLFOSO-SEEPXDQQSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 40580526
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0003686] Furanoid lignans
        • [CHEMONTID:0001604] Tetrahydrofuran lignans
          • [CHEMONTID:0003423] 7,7'-epoxylignans

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 GMXMKSFJQLFOSO-SEEPXDQQSA-N
Standard InCHI InChI=1S/C20H24O5/c1-11-12(2)20(14-6-8-16(22)18(10-14)24-4)25-19(11)13-5-7-15(21)17(9-13)23-3/h5-12,19-22H,1-4H3/t11-,12-,19+,20+/m0/s1
SMILES C[C@H]1[C@H](C)[C@H](c2ccc(c(c2)OC)O)O[C@H]1c1ccc(c(c1)OC)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
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota seeds n.a. n.a. PMID[17998162]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. n.a. PMID[1955885]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. fruit n.a. PMID[20879744]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. n.a. PMID[27419473]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. n.a. PMID[32515616]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. n.a. PMID[33444950]
NPO7237 Xanthostemon oppositifolius Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2665 Andinobates fulguritus Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8303 Catalpa bignonioides Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17811 Cephalonoplos segetum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5162 Comaster multifida Species Comatulidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8532 Helipterum tenellum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5334 Rhodotypos scandens Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6113 Piper pedicellosum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5746 Pancratium trianthum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO490 Lophozonia menziesii Species Nothofagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28409 Lens phaseoloides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19928 Lachnoanaerobaculum saburreum Species Lachnospiraceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO4539 Ipomoea cristulata Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1382 Hyptis tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7393 Esenbeckia nesiotica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota Aril n.a. n.a. Database[FooDB]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1382 Hyptis tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8303 Catalpa bignonioides Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO1382 Hyptis tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8303 Catalpa bignonioides Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1382 Hyptis tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[Title]
NPO5241 Myristica fragrans Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7237 Xanthostemon oppositifolius Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28409 Lens phaseoloides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8532 Helipterum tenellum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1382 Hyptis tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6113 Piper pedicellosum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5162 Comaster multifida Species Comatulidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19928 Lachnoanaerobaculum saburreum Species Lachnospiraceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4539 Ipomoea cristulata Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO490 Lophozonia menziesii Species Nothofagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17811 Cephalonoplos segetum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5746 Pancratium trianthum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7393 Esenbeckia nesiotica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5334 Rhodotypos scandens Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2665 Andinobates fulguritus Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8303 Catalpa bignonioides Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5241 Myristica fragrans Species Myristicaceae 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 NPC275152 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 NPC282703
1.0 High Similarity NPC184733
1.0 High Similarity NPC128208
1.0 High Similarity NPC129570
1.0 High Similarity NPC63238
1.0 High Similarity NPC602603
0.8293 Intermediate Similarity NPC11258
0.8293 Intermediate Similarity NPC21867
0.8293 Intermediate Similarity NPC487683
0.8293 Intermediate Similarity NPC45774
0.8293 Intermediate Similarity NPC74914
0.7907 Intermediate Similarity NPC488986
0.75 Intermediate Similarity NPC242807
0.75 Intermediate Similarity NPC153739
0.7391 Intermediate Similarity NPC142547
0.7391 Intermediate Similarity NPC228469
0.7073 Intermediate Similarity NPC142985
0.6667 Remote Similarity NPC115207
0.6667 Remote Similarity NPC158079
0.6667 Remote Similarity NPC228346
0.6667 Remote Similarity NPC40432
0.6667 Remote Similarity NPC161557
0.6591 Remote Similarity NPC147379
0.6591 Remote Similarity NPC469480
0.6296 Remote Similarity NPC77861
0.6222 Remote Similarity NPC158331
0.6087 Remote Similarity NPC126409
0.6087 Remote Similarity NPC99572
0.6087 Remote Similarity NPC487684
0.6047 Remote Similarity NPC204215
0.5893 Remote Similarity NPC487682
0.5789 Remote Similarity NPC176730
0.5789 Remote Similarity NPC123175
0.5714 Remote Similarity NPC27843
0.5714 Remote Similarity NPC478955
0.5714 Remote Similarity NPC478700
0.5714 Remote Similarity NPC7171
0.5682 Remote Similarity NPC209567
0.561 Remote Similarity NPC216929
0.561 Remote Similarity NPC312713
0.561 Remote Similarity NPC126935
0.561 Remote Similarity NPC65933
0.561 Remote Similarity NPC57268
0.561 Remote Similarity NPC172676
0.5532 Remote Similarity NPC470804
0.55 Remote Similarity NPC32163
0.549 Remote Similarity NPC135777
0.549 Remote Similarity NPC223185
0.549 Remote Similarity NPC610778
0.5435 Remote Similarity NPC4940
0.5385 Remote Similarity NPC181049
0.5357 Remote Similarity NPC471505
0.5319 Remote Similarity NPC175067
0.5283 Remote Similarity NPC471942
0.5263 Remote Similarity NPC7097
0.525 Remote Similarity NPC9891
0.525 Remote Similarity NPC88297
0.525 Remote Similarity NPC186845
0.525 Remote Similarity NPC156840
0.5238 Remote Similarity NPC160380
0.5238 Remote Similarity NPC159418
0.5238 Remote Similarity NPC38996
0.5238 Remote Similarity NPC36108
0.5238 Remote Similarity NPC233731
0.5238 Remote Similarity NPC610203
0.5185 Remote Similarity NPC272
0.5185 Remote Similarity NPC187998
0.5185 Remote Similarity NPC88640
0.5185 Remote Similarity NPC101153
0.5185 Remote Similarity NPC193666
0.5185 Remote Similarity NPC123526
0.5185 Remote Similarity NPC77040
0.5185 Remote Similarity NPC257582
0.5185 Remote Similarity NPC241522
0.5185 Remote Similarity NPC485398
0.5185 Remote Similarity NPC608725
0.5179 Remote Similarity NPC67247
0.5116 Remote Similarity NPC165133
0.5116 Remote Similarity NPC242885
0.5116 Remote Similarity NPC95614
0.5116 Remote Similarity NPC232316
0.5111 Remote Similarity NPC50683
0.5111 Remote Similarity NPC112571
0.5111 Remote Similarity NPC285725
0.5111 Remote Similarity NPC606519
0.5094 Remote Similarity NPC488988
0.5094 Remote Similarity NPC488984
0.5094 Remote Similarity NPC488985
0.5094 Remote Similarity NPC480701
0.5091 Remote Similarity NPC277804
0.5091 Remote Similarity NPC481088
0.5091 Remote Similarity NPC610652
0.5079 Remote Similarity NPC304048

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC275152 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
0.5227 Remote Similarity NPD824 Phase 4

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