Natural Product: NPC488737

Natural Product IDNPC488737
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
MCAHBPDMQOPNJI-FDILSSRTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 132566457
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 MCAHBPDMQOPNJI-FDILSSRTSA-N
Standard InCHI InChI=1S/C72H72O35/c1-24-49(82)57(90)65(71(98-24)104-63-53(86)45-37(80)18-33(76)20-39(45)100-61(63)28-7-14-32(75)15-8-28)106-69-59(92)55(88)51(84)41(102-69)22-96-67(94)47-43(26-3-10-30(73)11-4-26)44(27-5-12-31(74)13-6-27)48(47)68(95)97-23-42-52(85)56(89)60(93)70(103-42)107-66-58(91)50(83)25(2)99-72(66)105-64-54(87)46-38(81)19-34(77)21-40(46)101-62(64)29-9-16-35(78)36(79)17-29/h3-21,24-25,41-44,47-52,55-60,65-66,69-85,88-93H,22-23H2,1-2H3/t24-,25-,41+,42+,43-,44-,47+,48+,49-,50-,51+,52+,55-,56-,57+,58+,59+,60+,65+,66+,69-,70-,71-,72-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)Oc1c(=O)c2c(cc(cc2oc1c1ccc(cc1)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](COC(=O)[C@@H]2[C@@H](c3ccc(cc3)O)[C@H](c3ccc(cc3)O)[C@H]2C(=O)OC[C@@H]2[C@H]([C@@H]([C@H]([C@@H](O2)O[C@@H]2[C@@H]([C@H]([C@H](C)O[C@H]2Oc2c(=O)c3c(cc(cc3oc2c2ccc(c(c2)O)O)O)O)O)O)O)O)O)O1)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
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Leaves n.a. n.a. PMID[27140807]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota leaves n.a. n.a. PMID[33127538]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota fresh sarcotestas Kwanak Campus of Seoul National University, Seoul, Korea 1996-Sep PMID[9677265]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota leaves St. Louis 1996-SEP PMID[9834151]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. PMID[9834158]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Wood n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. Database[FooDB]

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
NPT519 Cell line SH-SY5Y Homo sapiens Activity = 96.7 % PMID[27140807]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 100000.0 nM PMID[27140807]

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 NPC488737 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
0.9794 High Similarity NPC488736
0.9794 High Similarity NPC488733
0.9588 High Similarity NPC488734
0.9588 High Similarity NPC488735
0.9588 High Similarity NPC488732
0.9588 High Similarity NPC488738
0.8641 High Similarity NPC488740
0.8447 Intermediate Similarity NPC488739
0.7071 Intermediate Similarity NPC95866
0.7019 Intermediate Similarity NPC122467
0.697 Remote Similarity NPC476215
0.6923 Remote Similarity NPC12013
0.6923 Remote Similarity NPC11432
0.6923 Remote Similarity NPC477613
0.6638 Remote Similarity NPC480444
0.6606 Remote Similarity NPC602448
0.6574 Remote Similarity NPC89127
0.6514 Remote Similarity NPC221342
0.6514 Remote Similarity NPC476470
0.6476 Remote Similarity NPC155877
0.6466 Remote Similarity NPC480445
0.6422 Remote Similarity NPC471669
0.641 Remote Similarity NPC162394
0.6393 Remote Similarity NPC473554
0.6381 Remote Similarity NPC163242
0.6381 Remote Similarity NPC272068
0.6364 Remote Similarity NPC21359
0.6364 Remote Similarity NPC460984
0.6316 Remote Similarity NPC303694
0.6281 Remote Similarity NPC25946
0.625 Remote Similarity NPC254855
0.625 Remote Similarity NPC116864
0.625 Remote Similarity NPC244776
0.625 Remote Similarity NPC94610
0.624 Remote Similarity NPC487502
0.6238 Remote Similarity NPC216496
0.6168 Remote Similarity NPC203259
0.6168 Remote Similarity NPC33054
0.6168 Remote Similarity NPC176740
0.6168 Remote Similarity NPC471725
0.6168 Remote Similarity NPC134532
0.6168 Remote Similarity NPC602582
0.6154 Remote Similarity NPC170052
0.6154 Remote Similarity NPC135846
0.6075 Remote Similarity NPC173582
0.6075 Remote Similarity NPC265885
0.6075 Remote Similarity NPC181465
0.6075 Remote Similarity NPC215710
0.6075 Remote Similarity NPC473438
0.6075 Remote Similarity NPC253788
0.6071 Remote Similarity NPC292929
0.6053 Remote Similarity NPC89052
0.6048 Remote Similarity NPC487499
0.6018 Remote Similarity NPC223426
0.5963 Remote Similarity NPC255157
0.5963 Remote Similarity NPC35167
0.5963 Remote Similarity NPC259896
0.5926 Remote Similarity NPC470405
0.5877 Remote Similarity NPC218161
0.5872 Remote Similarity NPC304741
0.5841 Remote Similarity NPC85751
0.5841 Remote Similarity NPC19240
0.5814 Remote Similarity NPC249560
0.5781 Remote Similarity NPC30011
0.578 Remote Similarity NPC67326
0.5758 Remote Similarity NPC487501
0.5752 Remote Similarity NPC142142
0.5727 Remote Similarity NPC156869
0.569 Remote Similarity NPC214621
0.569 Remote Similarity NPC34267
0.569 Remote Similarity NPC81042
0.5688 Remote Similarity NPC471079
0.5682 Remote Similarity NPC487500
0.5678 Remote Similarity NPC173837
0.5676 Remote Similarity NPC129264
0.5631 Remote Similarity NPC127546
0.5631 Remote Similarity NPC57625
0.5631 Remote Similarity NPC173637
0.5631 Remote Similarity NPC317489
0.5631 Remote Similarity NPC223424
0.5631 Remote Similarity NPC600591
0.5625 Remote Similarity NPC231787
0.5565 Remote Similarity NPC220173
0.5556 Remote Similarity NPC480442
0.5546 Remote Similarity NPC292019
0.5546 Remote Similarity NPC202908
0.5538 Remote Similarity NPC72554
0.5534 Remote Similarity NPC111929
0.5534 Remote Similarity NPC320283
0.5534 Remote Similarity NPC41121
0.5526 Remote Similarity NPC473327
0.552 Remote Similarity NPC209550
0.552 Remote Similarity NPC241781
0.5514 Remote Similarity NPC224530
0.5504 Remote Similarity NPC275977
0.5495 Remote Similarity NPC39834
0.5487 Remote Similarity NPC470125
0.5484 Remote Similarity NPC156785
0.5478 Remote Similarity NPC97119
0.5478 Remote Similarity NPC603079
0.5476 Remote Similarity NPC480443
0.547 Remote Similarity NPC470450
0.5462 Remote Similarity NPC189564
0.5446 Remote Similarity NPC605592
0.5405 Remote Similarity NPC258044
0.5405 Remote Similarity NPC217387
0.5391 Remote Similarity NPC37668
0.5391 Remote Similarity NPC270448
0.5378 Remote Similarity NPC203145
0.5373 Remote Similarity NPC97817
0.5372 Remote Similarity NPC480441
0.5372 Remote Similarity NPC25523
0.537 Remote Similarity NPC259957
0.5357 Remote Similarity NPC471748
0.5354 Remote Similarity NPC192539
0.5351 Remote Similarity NPC240306
0.5351 Remote Similarity NPC153755
0.5299 Remote Similarity NPC476472
0.5299 Remote Similarity NPC294815
0.5299 Remote Similarity NPC16194
0.5299 Remote Similarity NPC76831
0.5289 Remote Similarity NPC477895
0.5278 Remote Similarity NPC175107
0.5278 Remote Similarity NPC48093
0.5268 Remote Similarity NPC139320
0.5263 Remote Similarity NPC470444
0.5254 Remote Similarity NPC470445
0.5246 Remote Similarity NPC217520
0.5217 Remote Similarity NPC253521
0.5217 Remote Similarity NPC61904
0.5217 Remote Similarity NPC113836
0.5214 Remote Similarity NPC221288
0.5214 Remote Similarity NPC194836
0.5214 Remote Similarity NPC91493
0.5214 Remote Similarity NPC605081
0.5175 Remote Similarity NPC65563
0.5175 Remote Similarity NPC470949
0.5169 Remote Similarity NPC470447
0.514 Remote Similarity NPC145038
0.514 Remote Similarity NPC56077
0.514 Remote Similarity NPC281131
0.514 Remote Similarity NPC253662
0.514 Remote Similarity NPC179950
0.514 Remote Similarity NPC88789
0.514 Remote Similarity NPC491374
0.5133 Remote Similarity NPC29958
0.5133 Remote Similarity NPC609888
0.513 Remote Similarity NPC144097
0.5128 Remote Similarity NPC32641
0.5128 Remote Similarity NPC256188
0.5128 Remote Similarity NPC35119
0.5118 Remote Similarity NPC474522
0.5086 Remote Similarity NPC296018
0.5086 Remote Similarity NPC126784
0.5086 Remote Similarity NPC241423
0.5086 Remote Similarity NPC154741
0.5085 Remote Similarity NPC101399
0.5085 Remote Similarity NPC217822
0.5085 Remote Similarity NPC11847
0.5085 Remote Similarity NPC198938
0.5048 Remote Similarity NPC276222
0.5048 Remote Similarity NPC274618
0.5048 Remote Similarity NPC118284
0.5048 Remote Similarity NPC608147
0.5047 Remote Similarity NPC77672
0.5047 Remote Similarity NPC133671
0.5047 Remote Similarity NPC135391
0.5047 Remote Similarity NPC78263
0.5047 Remote Similarity NPC250069
0.5041 Remote Similarity NPC219043
0.504 Remote Similarity NPC139571
0.5035 Remote Similarity NPC33083

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC488737 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
0.6168 Remote Similarity NPD6797 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