Natural Product: NPC210015

Natural Product IDNPC210015
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 JJWCPVLNGCKJFV-UXXRCYHCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101193480
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

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 JJWCPVLNGCKJFV-UXXRCYHCSA-N
Standard InCHI InChI=1S/C15H20O7/c1-2-3-8-4-5-9(17)10(6-8)21-15-14(20)13(19)12(18)11(7-16)22-15/h2,4-6,11-20H,1,3,7H2/t11-,12-,13+,14-,15-/m1/s1
SMILES C=CCc1ccc(c(c1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   312.12 Volume:   301.869
?
Van der Waals volume.
Dense:   1.034 LogP:   0.347
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.882
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.276
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   13.0
TPSA:   119.61
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   5.0 Rings:   2.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.456 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.685 Fsp3:   0.467
MCE-18:   48.364
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.355 Fluc inhibitor:   0.06
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.041
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.073
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.376 Promiscuous compounds:   0.155

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.775 MDCK Permeability:   -4.968
Pgp-inhibitor:   0.001 Pgp-substrate:   0.002
PAMPA:   0.433
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.496
20% Bioavailability (F20%):   0.942 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.024 MRP1:   0.04
Plasma Protein Binding (PPB):   73.665% Volume Distribution (VD):   -0.182
Fu: 25.42%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.5
BSEP inhibitor:   0.025

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.002 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.577 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.011 CYP2D6-substrate:   0.096
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.09
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.01
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  3.866 Half-life (T1/2):  3.072

ADMET: Toxicity

hERG Blockers:  0.023 hERG Blockers (10um):  0.198
Human Hepatotoxicity (H-HT):  0.478 Drug-induced Liver Injury (DILI):  0.72
AMES Toxicity:  0.822 Rat Oral Acute Toxicity:  0.033
Maximum Recommended Daily Dose:  0.02 Skin Sensitization:  0.998
Carcinogencity:  0.246 Eye Corrosion:  0.006
Eye Irritation:  0.683 Respiratory Toxicity:  0.05
Drug-induced Neurotoxicity:  0.027 Ototoxicity:  0.809
Hematotoxicity:  0.164 Drug-induced Nephrotoxicity:  0.428
Genotoxicity:  0.186 RPMI-8226 Immunitoxicity:  0.064
A549 Cytotoxicity:  0.178 Hek293 Cytotoxicity:  0.17
BCF:   0.35
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   2.825
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.347
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.359
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[11908994]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. root n.a. PMID[1823989]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[31747281]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38791403]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[8594148]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26351 Agastache rugosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26351 Agastache rugosa Species Lamiaceae 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
NPT113 Cell line RAW264.7 Mus musculus IC50 = 4100.0 nM PMID[31747281]

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 NPC210015 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
0.7719 Intermediate Similarity NPC469661
0.7593 Intermediate Similarity NPC19470
0.7273 Intermediate Similarity NPC205054
0.6792 Remote Similarity NPC60589
0.6792 Remote Similarity NPC469708
0.6607 Remote Similarity NPC9912
0.6557 Remote Similarity NPC65530
0.6418 Remote Similarity NPC602810
0.6379 Remote Similarity NPC270849
0.6176 Remote Similarity NPC147596
0.6 Remote Similarity NPC9248
0.6 Remote Similarity NPC481303
0.5965 Remote Similarity NPC221090
0.5781 Remote Similarity NPC278961
0.5781 Remote Similarity NPC113680
0.5758 Remote Similarity NPC212770
0.5714 Remote Similarity NPC79957
0.5652 Remote Similarity NPC191046
0.5625 Remote Similarity NPC100389
0.5593 Remote Similarity NPC166168
0.5588 Remote Similarity NPC52277
0.5556 Remote Similarity NPC177035
0.5538 Remote Similarity NPC134260
0.5536 Remote Similarity NPC192810
0.5522 Remote Similarity NPC189115
0.5522 Remote Similarity NPC106944
0.5517 Remote Similarity NPC12308
0.5484 Remote Similarity NPC214910
0.5484 Remote Similarity NPC65942
0.5484 Remote Similarity NPC248307
0.5469 Remote Similarity NPC59324
0.5469 Remote Similarity NPC473045
0.5469 Remote Similarity NPC97326
0.5467 Remote Similarity NPC299706
0.5467 Remote Similarity NPC115466
0.5467 Remote Similarity NPC61604
0.5455 Remote Similarity NPC142319
0.5455 Remote Similarity NPC186418
0.5455 Remote Similarity NPC202700
0.54 Remote Similarity NPC257124
0.5397 Remote Similarity NPC105827
0.5362 Remote Similarity NPC116229
0.5357 Remote Similarity NPC484157
0.5325 Remote Similarity NPC185307
0.5325 Remote Similarity NPC163635
0.5323 Remote Similarity NPC472024
0.5303 Remote Similarity NPC242028
0.5303 Remote Similarity NPC203230
0.5294 Remote Similarity NPC210192
0.5278 Remote Similarity NPC199459
0.5263 Remote Similarity NPC294470
0.5256 Remote Similarity NPC486549
0.5256 Remote Similarity NPC486547
0.5256 Remote Similarity NPC470235
0.5246 Remote Similarity NPC40377
0.5246 Remote Similarity NPC310661
0.5231 Remote Similarity NPC85799
0.5231 Remote Similarity NPC303422
0.5217 Remote Similarity NPC177742
0.5205 Remote Similarity NPC232228
0.52 Remote Similarity NPC469586
0.519 Remote Similarity NPC486546
0.5179 Remote Similarity NPC212729
0.5179 Remote Similarity NPC604498
0.5167 Remote Similarity NPC69513
0.5152 Remote Similarity NPC478871
0.5152 Remote Similarity NPC478870
0.5152 Remote Similarity NPC478872
0.5152 Remote Similarity NPC307110
0.5152 Remote Similarity NPC478873
0.5152 Remote Similarity NPC157554
0.5147 Remote Similarity NPC121001
0.5143 Remote Similarity NPC148273
0.5139 Remote Similarity NPC51328
0.5139 Remote Similarity NPC55158
0.5132 Remote Similarity NPC199928
0.5128 Remote Similarity NPC476868
0.5088 Remote Similarity NPC269242
0.5077 Remote Similarity NPC25292
0.5075 Remote Similarity NPC252169
0.5072 Remote Similarity NPC98777
0.5072 Remote Similarity NPC475096
0.507 Remote Similarity NPC21902
0.507 Remote Similarity NPC186406
0.507 Remote Similarity NPC88043
0.5068 Remote Similarity NPC38041
0.5068 Remote Similarity NPC18979
0.5068 Remote Similarity NPC22150
0.5068 Remote Similarity NPC257963
0.5067 Remote Similarity NPC476203

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC210015 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
0.54 Remote Similarity NPD228 Phase 0

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