Natural Product: NPC17215

Natural Product IDNPC17215
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 UFWGANQPWYXUQI-FDNTWFBCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 72551450
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003531] Flavonoid-3-O-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 UFWGANQPWYXUQI-FDNTWFBCSA-N
Standard InCHI InChI=1S/C22H22O12/c1-7-15(26)18(29)19(30)22(32-7)34-21-17(28)14-10(24)5-9(23)6-12(14)33-20(21)8-3-11(25)16(27)13(4-8)31-2/h3-7,15,18-19,22-27,29-30H,1-2H3/t7-,15-,18+,19+,22-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)Oc1c(=O)c2c(cc(cc2oc1c1cc(c(c(c1)OC)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   478.11 Volume:   439.233
?
Van der Waals volume.
Dense:   1.089 LogP:   0.98
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.288
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.388
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   199.51
?
Topological Polar Surface Area.
 H-Bond Acceptor:   12.0
H-Bond Donor:   7.0 Rings:   4.0
Heavy Atoms:   12.0

MedChem Properties

QED Drug-Likeness Score:   0.257 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.097 Fsp3:   0.318
MCE-18:   93.655
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.565 Fluc inhibitor:   0.145
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.913
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.869
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.117 Promiscuous compounds:   0.845

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.149 MDCK Permeability:   -5.221
Pgp-inhibitor:   0.005 Pgp-substrate:   0.449
PAMPA:   0.969
?
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):   0.068
20% Bioavailability (F20%):   0.198 30% Bioavailability (F30%):   0.864
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.202
Plasma Protein Binding (PPB):   87.895% Volume Distribution (VD):   -0.086
Fu: 10.596%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.977
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.98
BSEP inhibitor:   0.348

ADMET: Metabolism

CYP1A2-inhibitor:   0.007 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.013 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.316
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.145
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.904
?
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):  3.053 Half-life (T1/2):  3.259

ADMET: Toxicity

hERG Blockers:  0.029 hERG Blockers (10um):  0.449
Human Hepatotoxicity (H-HT):  0.431 Drug-induced Liver Injury (DILI):  0.682
AMES Toxicity:  0.652 Rat Oral Acute Toxicity:  0.08
Maximum Recommended Daily Dose:  0.247 Skin Sensitization:  0.951
Carcinogencity:  0.162 Eye Corrosion:  0.001
Eye Irritation:  0.874 Respiratory Toxicity:  0.097
Drug-induced Neurotoxicity:  0.004 Ototoxicity:  0.685
Hematotoxicity:  0.047 Drug-induced Nephrotoxicity:  0.09
Genotoxicity:  0.782 RPMI-8226 Immunitoxicity:  0.063
A549 Cytotoxicity:  0.443 Hek293 Cytotoxicity:  0.476
BCF:   0.686
?
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:   3.39
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.684
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.939
?
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
NPO996 Acacia confusa Species Fabaceae Eukaryota leaves n.a. n.a. PMID[10843598]
NPO996 Acacia confusa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[20047272]
NPO5664 Davallia mariesii Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2851 Acanthella acuta Species Axinellidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO996 Acacia confusa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1919 Erica arborea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4725 Isodon lihsienensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5664 Davallia mariesii Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1919 Erica arborea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5664 Davallia mariesii Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1919 Erica arborea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4725 Isodon lihsienensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1919 Erica arborea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5664 Davallia mariesii Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO996 Acacia confusa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6619 Phoebe clemensii Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1919 Erica arborea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2851 Acanthella acuta Species Axinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO66 Siphula decumbens Species Icmadophilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4725 Isodon lihsienensis 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

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 NPC17215 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
0.8082 Intermediate Similarity NPC135599
0.8082 Intermediate Similarity NPC73855
0.8082 Intermediate Similarity NPC113968
0.8082 Intermediate Similarity NPC328940
0.8082 Intermediate Similarity NPC277174
0.8082 Intermediate Similarity NPC606877
0.8052 Intermediate Similarity NPC223747
0.7973 Intermediate Similarity NPC127546
0.7973 Intermediate Similarity NPC57625
0.7973 Intermediate Similarity NPC173637
0.7973 Intermediate Similarity NPC317489
0.7973 Intermediate Similarity NPC223424
0.7973 Intermediate Similarity NPC600591
0.7867 Intermediate Similarity NPC265530
0.7792 Intermediate Similarity NPC219904
0.76 Intermediate Similarity NPC111929
0.76 Intermediate Similarity NPC320283
0.76 Intermediate Similarity NPC41121
0.7215 Intermediate Similarity NPC325555
0.7215 Intermediate Similarity NPC226304
0.6867 Remote Similarity NPC203050
0.6867 Remote Similarity NPC225434
0.6835 Remote Similarity NPC19388
0.6835 Remote Similarity NPC240431
0.6835 Remote Similarity NPC55786
0.6824 Remote Similarity NPC609888
0.6778 Remote Similarity NPC476472
0.6778 Remote Similarity NPC294815
0.6778 Remote Similarity NPC16194
0.675 Remote Similarity NPC145038
0.675 Remote Similarity NPC56077
0.675 Remote Similarity NPC281131
0.675 Remote Similarity NPC253662
0.675 Remote Similarity NPC179950
0.675 Remote Similarity NPC88789
0.675 Remote Similarity NPC491374
0.6744 Remote Similarity NPC39834
0.6707 Remote Similarity NPC175107
0.6667 Remote Similarity NPC203259
0.6667 Remote Similarity NPC305811
0.6667 Remote Similarity NPC33054
0.6667 Remote Similarity NPC176740
0.6667 Remote Similarity NPC471725
0.6667 Remote Similarity NPC134532
0.6667 Remote Similarity NPC602582
0.6627 Remote Similarity NPC120099
0.6585 Remote Similarity NPC472459
0.6556 Remote Similarity NPC473327
0.6543 Remote Similarity NPC158674
0.6517 Remote Similarity NPC153755
0.6477 Remote Similarity NPC605592
0.6463 Remote Similarity NPC271692
0.6456 Remote Similarity NPC34531
0.642 Remote Similarity NPC77672
0.642 Remote Similarity NPC133671
0.642 Remote Similarity NPC135391
0.642 Remote Similarity NPC78263
0.642 Remote Similarity NPC250069
0.6395 Remote Similarity NPC116864
0.6395 Remote Similarity NPC244776
0.6375 Remote Similarity NPC67037
0.6375 Remote Similarity NPC255615
0.6364 Remote Similarity NPC173582
0.6364 Remote Similarity NPC265885
0.6364 Remote Similarity NPC181465
0.6364 Remote Similarity NPC215710
0.6364 Remote Similarity NPC473438
0.6364 Remote Similarity NPC253788
0.6341 Remote Similarity NPC64305
0.631 Remote Similarity NPC60735
0.631 Remote Similarity NPC26230
0.6265 Remote Similarity NPC46420
0.6265 Remote Similarity NPC52550
0.6265 Remote Similarity NPC27640
0.6265 Remote Similarity NPC349108
0.6235 Remote Similarity NPC609478
0.6207 Remote Similarity NPC95866
0.619 Remote Similarity NPC59534
0.6118 Remote Similarity NPC182121
0.6118 Remote Similarity NPC611303
0.6064 Remote Similarity NPC220173
0.6049 Remote Similarity NPC288084
0.6049 Remote Similarity NPC276222
0.6049 Remote Similarity NPC274618
0.6049 Remote Similarity NPC118284
0.6049 Remote Similarity NPC608147
0.6024 Remote Similarity NPC249281
0.6 Remote Similarity NPC471748
0.6 Remote Similarity NPC67326
0.5977 Remote Similarity NPC209023
0.5934 Remote Similarity NPC155877
0.5934 Remote Similarity NPC156869
0.5909 Remote Similarity NPC476215
0.5904 Remote Similarity NPC476771
0.5889 Remote Similarity NPC29958
0.5833 Remote Similarity NPC476772
0.5823 Remote Similarity NPC268668
0.5816 Remote Similarity NPC89052
0.5795 Remote Similarity NPC605784
0.5747 Remote Similarity NPC159579
0.5732 Remote Similarity NPC54802
0.5732 Remote Similarity NPC197304
0.573 Remote Similarity NPC355481
0.5714 Remote Similarity NPC471079
0.5714 Remote Similarity NPC139320
0.57 Remote Similarity NPC173837
0.5686 Remote Similarity NPC139571
0.5684 Remote Similarity NPC122467
0.5684 Remote Similarity NPC37668
0.5667 Remote Similarity NPC265115
0.5652 Remote Similarity NPC163242
0.5652 Remote Similarity NPC272068
0.5644 Remote Similarity NPC217520
0.5638 Remote Similarity NPC126784
0.5638 Remote Similarity NPC241423
0.5632 Remote Similarity NPC42773
0.5632 Remote Similarity NPC138927
0.5632 Remote Similarity NPC45522
0.5632 Remote Similarity NPC599850
0.5618 Remote Similarity NPC116458
0.5618 Remote Similarity NPC246943
0.5604 Remote Similarity NPC480463
0.5604 Remote Similarity NPC278419
0.5604 Remote Similarity NPC179198
0.5579 Remote Similarity NPC470443
0.5568 Remote Similarity NPC235260
0.5568 Remote Similarity NPC155763
0.5568 Remote Similarity NPC129217
0.5567 Remote Similarity NPC471669
0.5567 Remote Similarity NPC89127
0.5556 Remote Similarity NPC276377
0.5556 Remote Similarity NPC66087
0.5545 Remote Similarity NPC292019
0.5545 Remote Similarity NPC202908
0.5543 Remote Similarity NPC480466
0.5532 Remote Similarity NPC129264
0.5521 Remote Similarity NPC270448
0.5506 Remote Similarity NPC101026
0.5506 Remote Similarity NPC488077
0.5506 Remote Similarity NPC189913
0.5495 Remote Similarity NPC254855
0.5495 Remote Similarity NPC94610
0.5484 Remote Similarity NPC196127
0.5474 Remote Similarity NPC470125
0.5455 Remote Similarity NPC216496
0.5455 Remote Similarity NPC223426
0.5455 Remote Similarity NPC133953
0.5435 Remote Similarity NPC251417
0.5417 Remote Similarity NPC12013
0.5417 Remote Similarity NPC483414
0.5417 Remote Similarity NPC11432
0.5417 Remote Similarity NPC483415
0.5417 Remote Similarity NPC477613
0.54 Remote Similarity NPC81042
0.5392 Remote Similarity NPC477895
0.5376 Remote Similarity NPC258044
0.5376 Remote Similarity NPC217387
0.5368 Remote Similarity NPC473571
0.5368 Remote Similarity NPC110941
0.5361 Remote Similarity NPC483416
0.5361 Remote Similarity NPC606657
0.5347 Remote Similarity NPC203145
0.5341 Remote Similarity NPC488080
0.5341 Remote Similarity NPC169977
0.5333 Remote Similarity NPC286342
0.5333 Remote Similarity NPC601710
0.5327 Remote Similarity NPC156785
0.5326 Remote Similarity NPC4390
0.5321 Remote Similarity NPC192539
0.5312 Remote Similarity NPC154741
0.5306 Remote Similarity NPC64755
0.5294 Remote Similarity NPC189564
0.5275 Remote Similarity NPC88023
0.5275 Remote Similarity NPC206123
0.5275 Remote Similarity NPC309025
0.5263 Remote Similarity NPC65563
0.5263 Remote Similarity NPC470949
0.5263 Remote Similarity NPC150164
0.5258 Remote Similarity NPC245452
0.5256 Remote Similarity NPC279989
0.5253 Remote Similarity NPC85751
0.5253 Remote Similarity NPC19240
0.5248 Remote Similarity NPC214621
0.5248 Remote Similarity NPC34267
0.5243 Remote Similarity NPC219043
0.5243 Remote Similarity NPC48984
0.5227 Remote Similarity NPC136042
0.5222 Remote Similarity NPC191306
0.5222 Remote Similarity NPC488071
0.5217 Remote Similarity NPC170052
0.5217 Remote Similarity NPC135846
0.5208 Remote Similarity NPC35167
0.5208 Remote Similarity NPC186816
0.52 Remote Similarity NPC221342
0.52 Remote Similarity NPC470445
0.52 Remote Similarity NPC476470
0.5192 Remote Similarity NPC303694
0.5172 Remote Similarity NPC473043
0.5169 Remote Similarity NPC84362
0.5165 Remote Similarity NPC85707

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC17215 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
0.6667 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