Natural Product: NPC210330

Natural Product IDNPC210330
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Prismatomerin
IUPAC Name n.a.
Synonyms Prismatomerin
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL250261
PubChem CID 23625548
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones

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 CAASUWFDLSGDTI-WEZSCGFBSA-N
Standard InCHI InChI=1S/C20H16O7/c1-24-17(22)14-9-25-19-15-12(14)6-7-20(15)16(26-19)13(18(23)27-20)8-10-2-4-11(21)5-3-10/h2-9,12,15-16,19,21H,1H3/b13-8+/t12-,15-,16+,19-,20+/m1/s1
SMILES COC(=O)C1=CO[C@H]2[C@H]3[C@@H]1C=C[C@]13[C@H](/C(=Cc3ccc(cc3)O)/C(=O)O1)O2

  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
NPO6568 Prismatomeris tetrandra Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[17665951]
NPO6568 Prismatomeris tetrandra Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6568 Prismatomeris tetrandra Species Rubiaceae 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
NPT90 Cell line DU-145 Homo sapiens GI50 = 114.82 nM PMID[23734701]
NPT402 Cell line Hs-578T Homo sapiens GI50 = 257.04 nM Open TG-GATES in vivo data: Biochemistry
NPT83 Cell line MCF7 Homo sapiens GI50 = 120.23 nM PMID[9213587]
NPT82 Cell line MDA-MB-231 Homo sapiens GI50 = 162.18 nM PMID[18951808]
NPT378 Cell line NCI/ADR-RES Homo sapiens GI50 = 169.82 nM PMID[18951808]
NPT386 Cell line KM12 Homo sapiens GI50 = 302.0 nM PMID[17125224]
NPT1460 Cell line L929 Mus musculus IC50 = 210.0 nM PMID[18505859]
NPT81 Cell line A549 Homo sapiens IC50 = 1410.0 nM PMID[18053715]
NPT660 Cell line SW480 Homo sapiens IC50 = 60.0 nM PMID[23066712]
NPT404 Cell line CCRF-CEM Homo sapiens GI50 = 38.02 nM DrugMatrix in vitro pharmacology data
NPT116 Cell line HL-60 Homo sapiens GI50 > 10.0 nM DrugMatrix in vitro pharmacology data
NPT111 Cell line K562 Homo sapiens GI50 > 10.0 nM PMID[17696332]
NPT112 Cell line MOLT-4 Homo sapiens GI50 > 10.0 nM PMID[25264585]
NPT389 Cell line RPMI-8226 Homo sapiens GI50 > 10.0 nM PMID[17049251]
NPT385 Cell line SR Homo sapiens GI50 = 10.47 nM PMID[17049251]
NPT81 Cell line A549 Homo sapiens GI50 = 295.12 nM PMID[9514009]
NPT394 Cell line EKVX Homo sapiens GI50 = 354.81 nM PMID[9514009]
NPT379 Cell line HOP-62 Homo sapiens GI50 = 263.03 nM PMID[9514009]
NPT405 Cell line NCI-H226 Homo sapiens GI50 = 173.78 nM PMID[9514009]
NPT370 Cell line NCI-H23 Homo sapiens GI50 = 186.21 nM PMID[9514009]
NPT397 Cell line NCI-H460 Homo sapiens GI50 = 239.88 nM PMID[9514009]
NPT455 Cell line NCI-H522 Homo sapiens GI50 = 186.21 nM PMID[9514009]
NPT407 Cell line COLO 205 Homo sapiens GI50 = 537.03 nM PMID[25747495]
NPT393 Cell line HCT-116 Homo sapiens GI50 > 10.0 nM PMID[25747495]
NPT148 Cell line HCT-15 Homo sapiens GI50 = 162.18 nM PMID[25747495]
NPT139 Cell line HT-29 Homo sapiens GI50 = 107.15 nM PMID[25730346]
NPT323 Cell line SW-620 Homo sapiens GI50 > 10.0 nM DrugMatrix in vitro pharmacology data
NPT395 Cell line SF-268 Homo sapiens GI50 = 263.03 nM PMID[25681711]
NPT399 Cell line SF-295 Homo sapiens GI50 = 588.84 nM PMID[25747495]
NPT374 Cell line SF-539 Homo sapiens GI50 = 257.04 nM PMID[25747495]
NPT383 Cell line SNB-19 Homo sapiens GI50 = 346.74 nM PMID[25747495]
NPT380 Cell line U-251 Homo sapiens GI50 = 295.12 nM PMID[16562843]
NPT390 Cell line LOX IMVI Homo sapiens GI50 = 20.89 nM PMID[16562843]
NPT375 Cell line Malme-3M Homo sapiens GI50 = 134.9 nM PMID[17900165]
NPT387 Cell line M14 Homo sapiens GI50 = 162.18 nM PMID[16309317]
NPT147 Cell line SK-MEL-2 Homo sapiens GI50 = 165.96 nM PMID[14640534]
NPT170 Cell line SK-MEL-28 Homo sapiens GI50 = 316.23 nM PMID[14640534]
NPT373 Cell line SK-MEL-5 Homo sapiens GI50 > 10.0 nM PMID[14640534]
NPT403 Cell line UACC-257 Homo sapiens GI50 = 144.54 nM PMID[14640534]
NPT398 Cell line UACC-62 Homo sapiens GI50 = 436.52 nM PMID[15043411]
NPT458 Cell line IGROV-1 Homo sapiens GI50 = 501.19 nM PMID[14640534]
NPT456 Cell line OVCAR-4 Homo sapiens GI50 = 575.44 nM PMID[9514009]
NPT382 Cell line OVCAR-5 Homo sapiens GI50 = 257.04 nM DrugMatrix in vivo data: Biochemistry
NPT381 Cell line OVCAR-8 Homo sapiens GI50 = 173.78 nM PMID[20014752]
NPT146 Cell line SK-OV-3 Homo sapiens GI50 = 912.01 nM PMID[20553011]
NPT401 Cell line 786-0 Homo sapiens GI50 = 19.5 nM PMID[20843939]
NPT376 Cell line A498 Homo sapiens GI50 = 234.42 nM PubChem BioAssay data set
NPT369 Cell line ACHN Homo sapiens GI50 > 10.0 nM PubChem BioAssay data set
NPT308 Cell line CAKI-1 Homo sapiens GI50 = 125.89 nM PubChem BioAssay data set
NPT406 Cell line RXF 393 Homo sapiens GI50 > 10.0 nM PubChem BioAssay data set
NPT368 Cell line SN12C Homo sapiens GI50 = 173.78 nM PMID[25278237]
NPT384 Cell line TK-10 Homo sapiens GI50 = 288.4 nM PMID[25278237]
NPT371 Cell line UO-31 Homo sapiens GI50 = 120.23 nM PMID[12444684]
NPT306 Cell line PC-3 Homo sapiens GI50 = 169.82 nM PMID[25278237]
NPT457 Cell line BT-549 Homo sapiens GI50 = 151.36 nM PMID[19006372]
NPT396 Cell line T47D Homo sapiens GI50 = 380.19 nM PMID[19006372]
NPT385 Cell line SR Homo sapiens TGI = 467.74 nM PMID[15974608]
NPT81 Cell line A549 Homo sapiens TGI = 831.76 nM PMID[22168134]
NPT379 Cell line HOP-62 Homo sapiens TGI = 707.95 nM PMID[17844994]
NPT405 Cell line NCI-H226 Homo sapiens TGI = 478.63 nM PMID[17844994]
NPT393 Cell line HCT-116 Homo sapiens TGI = 100.0 nM PMID[15730245]
NPT148 Cell line HCT-15 Homo sapiens TGI = 575.44 nM PMID[22168134]
NPT386 Cell line KM12 Homo sapiens TGI = 1513.56 nM PMID[16309305]
NPT395 Cell line SF-268 Homo sapiens TGI = 758.58 nM PMID[23865778]
NPT374 Cell line SF-539 Homo sapiens TGI = 457.09 nM PMID[23822585]
NPT383 Cell line SNB-19 Homo sapiens TGI = 109647.82 nM PMID[19216517]
NPT380 Cell line U-251 Homo sapiens TGI = 954.99 nM PMID[19216517]
NPT390 Cell line LOX IMVI Homo sapiens TGI = 239.88 nM PMID[19216517]
NPT373 Cell line SK-MEL-5 Homo sapiens TGI = 186.21 nM PMID[19216517]
NPT458 Cell line IGROV-1 Homo sapiens TGI = 371.54 nM PMID[19216517]
NPT456 Cell line OVCAR-4 Homo sapiens TGI = 3467.37 nM PMID[23822585]
NPT382 Cell line OVCAR-5 Homo sapiens TGI = 407.38 nM PMID[19388709]
NPT381 Cell line OVCAR-8 Homo sapiens TGI = 501.19 nM PMID[17844994]
NPT146 Cell line SK-OV-3 Homo sapiens TGI = 3162.28 nM PMID[17844994]
NPT401 Cell line 786-0 Homo sapiens TGI = 194.98 nM PMID[17844994]
NPT376 Cell line A498 Homo sapiens TGI = 457.09 nM PMID[17844994]
NPT308 Cell line CAKI-1 Homo sapiens TGI = 501.19 nM PMID[17844994]
NPT406 Cell line RXF 393 Homo sapiens TGI = 162.18 nM PMID[17844994]
NPT368 Cell line SN12C Homo sapiens TGI = 380.19 nM PMID[20045651]
NPT83 Cell line MCF7 Homo sapiens TGI = 1000.0 nM PMID[17844994]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. GI50 = 199.53 nM PMID[17665951]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 410.0 nM PMID[17665951]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. GI50 = 1949.84 nM PMID[17665951]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. GI50 = 489.78 nM PMID[17665951]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. TGI = 5370.32 nM PMID[17665951]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. TGI = 562.34 nM PMID[17665951]

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 LD50 = 195.0 nM PMID[11421746]

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 NPC210330 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
0.791 Intermediate Similarity NPC76211
0.7463 Intermediate Similarity NPC473428
0.6032 Remote Similarity NPC305157
0.6032 Remote Similarity NPC307846

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC210330 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