Natural Product: NPC606629

Natural Product IDNPC606629
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 NQWVSMVXKMHKTF-HZPDHXFCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL4639246
PubChem CID n.a.
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 NQWVSMVXKMHKTF-HZPDHXFCSA-N
Standard InCHI InChI=1S/C21H24O6/c1-24-18-7-5-13(11-20(18)26-3)8-15-12-27-21(23)16(15)9-14-4-6-17(22)19(10-14)25-2/h4-7,10-11,15-16,22H,8-9,12H2,1-3H3/t15-,16-/m1/s1
SMILES COc1cc(C[C@H]2C(=O)OC[C@H]2Cc2ccc(OC)c(OC)c2)ccc1O

  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
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. root n.a. PMID[15635251]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. root n.a. PMID[24660446]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[501363]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[7320737]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3837 Wikstroemia indica Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3837 Wikstroemia indica Species Thymelaeaceae 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
NPT116 Cell line HL-60 Homo sapiens IC50 = 13000.0 nM PMID[32359854]
NPT28438 Unchecked Unchecked n.a. IC50 > 100000.0 nM PMID[32359854]
NPT28438 Unchecked Unchecked n.a. IC50 = 57000.0 nM PMID[32359854]

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 NPC606629 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 NPC300776
1.0 High Similarity NPC176814
1.0 High Similarity NPC4982
0.8776 High Similarity NPC68779
0.8776 High Similarity NPC108598
0.8491 Intermediate Similarity NPC106920
0.8491 Intermediate Similarity NPC15811
0.8448 Intermediate Similarity NPC478703
0.8448 Intermediate Similarity NPC478704
0.8393 Intermediate Similarity NPC282291
0.8393 Intermediate Similarity NPC166137
0.8113 Intermediate Similarity NPC273657
0.7818 Intermediate Similarity NPC5310
0.7755 Intermediate Similarity NPC223807
0.7627 Intermediate Similarity NPC216223
0.717 Intermediate Similarity NPC211386
0.6957 Remote Similarity NPC299706
0.6957 Remote Similarity NPC115466
0.6957 Remote Similarity NPC61604
0.6833 Remote Similarity NPC145569
0.6825 Remote Similarity NPC478705
0.6786 Remote Similarity NPC205915
0.6452 Remote Similarity NPC487679
0.6452 Remote Similarity NPC487678
0.6441 Remote Similarity NPC102908
0.6429 Remote Similarity NPC487680
0.6415 Remote Similarity NPC227217
0.6415 Remote Similarity NPC117780
0.629 Remote Similarity NPC31751
0.623 Remote Similarity NPC100675
0.623 Remote Similarity NPC601691
0.6182 Remote Similarity NPC607444
0.6071 Remote Similarity NPC110958
0.6071 Remote Similarity NPC19890
0.6066 Remote Similarity NPC110699
0.6066 Remote Similarity NPC106055
0.6038 Remote Similarity NPC31344
0.6038 Remote Similarity NPC317769
0.6038 Remote Similarity NPC72796
0.6 Remote Similarity NPC176586
0.6 Remote Similarity NPC210354
0.5968 Remote Similarity NPC293757
0.5968 Remote Similarity NPC668
0.5902 Remote Similarity NPC191158
0.5902 Remote Similarity NPC177644
0.5873 Remote Similarity NPC485282
0.5873 Remote Similarity NPC485283
0.5873 Remote Similarity NPC485281
0.5811 Remote Similarity NPC245615
0.5797 Remote Similarity NPC158635
0.5797 Remote Similarity NPC229882
0.5714 Remote Similarity NPC606339
0.5692 Remote Similarity NPC64201
0.5625 Remote Similarity NPC610284
0.5606 Remote Similarity NPC169973
0.5522 Remote Similarity NPC120852
0.5522 Remote Similarity NPC174512
0.5424 Remote Similarity NPC92693
0.541 Remote Similarity NPC275950
0.5385 Remote Similarity NPC81067
0.5385 Remote Similarity NPC67247
0.5385 Remote Similarity NPC602945
0.5373 Remote Similarity NPC608199
0.5333 Remote Similarity NPC274356
0.5333 Remote Similarity NPC173308
0.5333 Remote Similarity NPC181079
0.5333 Remote Similarity NPC40237
0.5333 Remote Similarity NPC101748
0.5323 Remote Similarity NPC253481
0.5323 Remote Similarity NPC253722
0.5263 Remote Similarity NPC325295
0.5263 Remote Similarity NPC76308
0.519 Remote Similarity NPC486549
0.519 Remote Similarity NPC486548
0.5125 Remote Similarity NPC486546
0.5094 Remote Similarity NPC165133
0.5094 Remote Similarity NPC242885
0.5094 Remote Similarity NPC95614
0.5094 Remote Similarity NPC232316
0.5079 Remote Similarity NPC475875
0.5077 Remote Similarity NPC610652
0.5075 Remote Similarity NPC29599

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC606629 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