Natural Product: NPC95159

Natural Product IDNPC95159
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 FOHXFLPXBUAOJM-JUHDPVRTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 72551438
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 FOHXFLPXBUAOJM-JUHDPVRTSA-N
Standard InCHI InChI=1S/C21H20O13/c22-5-12-15(28)17(30)18(31)21(33-12)34-20-16(29)13-8(24)3-7(23)4-11(13)32-19(20)6-1-9(25)14(27)10(26)2-6/h1-4,12,15,17-18,21-28,30-31H,5H2/t12-,15+,17+,18-,21+/m0/s1
SMILES c1c(cc(c(c1O)O)O)c1c(c(=O)c2c(cc(cc2o1)O)O)O[C@@H]1[C@H]([C@@H]([C@@H]([C@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   480.09 Volume:   430.728
?
Van der Waals volume.
Dense:   1.115 LogP:   0.213
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.75
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.564
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   230.74
?
Topological Polar Surface Area.
 H-Bond Acceptor:   13.0
H-Bond Donor:   9.0 Rings:   4.0
Heavy Atoms:   13.0

MedChem Properties

QED Drug-Likeness Score:   0.208 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.146 Fsp3:   0.286
MCE-18:   94.37
?
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:   1
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.726 Fluc inhibitor:   0.225
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.918
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.59
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.31 Promiscuous compounds:   0.935

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.403 MDCK Permeability:   -4.804
Pgp-inhibitor:   0.0 Pgp-substrate:   0.636
PAMPA:   1.0
?
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):   0.066
20% Bioavailability (F20%):   0.597 30% Bioavailability (F30%):   0.995
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.048
Plasma Protein Binding (PPB):   82.954% Volume Distribution (VD):   0.016
Fu: 15.624%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.914
OATP1B3 inhibitor:   0.988 BCRP inhibitor:   0.918
BSEP inhibitor:   0.086

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.015
CYP2C9-inhibitor:   0.006 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.004 CYP2D6-substrate:   0.974
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.962
?
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):  3.034 Half-life (T1/2):  3.624

ADMET: Toxicity

hERG Blockers:  0.007 hERG Blockers (10um):  0.423
Human Hepatotoxicity (H-HT):  0.363 Drug-induced Liver Injury (DILI):  0.71
AMES Toxicity:  0.647 Rat Oral Acute Toxicity:  0.069
Maximum Recommended Daily Dose:  0.245 Skin Sensitization:  1.0
Carcinogencity:  0.072 Eye Corrosion:  0.0
Eye Irritation:  0.963 Respiratory Toxicity:  0.052
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.963
Hematotoxicity:  0.011 Drug-induced Nephrotoxicity:  0.012
Genotoxicity:  0.91 RPMI-8226 Immunitoxicity:  0.012
A549 Cytotoxicity:  0.955 Hek293 Cytotoxicity:  0.26
BCF:   0.515
?
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:   3.173
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.448
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.758
?
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
NPO15339 Artemisia afra Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO27910 Calea ternifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8843 Epipactis palustris Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15339 Artemisia afra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15050 Rumex obtusifolius Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15050 Rumex obtusifolius Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15050 Rumex obtusifolius Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8843 Epipactis palustris Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15050 Rumex obtusifolius Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2373 Popillia japonica Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15339 Artemisia afra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27910 Calea ternifolia Species Asteraceae 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 NPC95159 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 NPC19388
1.0 High Similarity NPC240431
1.0 High Similarity NPC55786
0.8939 High Similarity NPC34531
0.8696 High Similarity NPC145038
0.8696 High Similarity NPC56077
0.8696 High Similarity NPC281131
0.8696 High Similarity NPC253662
0.8696 High Similarity NPC179950
0.8696 High Similarity NPC88789
0.8696 High Similarity NPC491374
0.8406 Intermediate Similarity NPC135599
0.8406 Intermediate Similarity NPC73855
0.8406 Intermediate Similarity NPC113968
0.8406 Intermediate Similarity NPC328940
0.8406 Intermediate Similarity NPC277174
0.8406 Intermediate Similarity NPC606877
0.8286 Intermediate Similarity NPC77672
0.8286 Intermediate Similarity NPC133671
0.8286 Intermediate Similarity NPC135391
0.8286 Intermediate Similarity NPC78263
0.8286 Intermediate Similarity NPC250069
0.8169 Intermediate Similarity NPC64305
0.7945 Intermediate Similarity NPC472459
0.7945 Intermediate Similarity NPC325555
0.7945 Intermediate Similarity NPC226304
0.7838 Intermediate Similarity NPC60735
0.7838 Intermediate Similarity NPC26230
0.7746 Intermediate Similarity NPC67037
0.7746 Intermediate Similarity NPC255615
0.7733 Intermediate Similarity NPC120099
0.7532 Intermediate Similarity NPC203050
0.7532 Intermediate Similarity NPC225434
0.7397 Intermediate Similarity NPC476771
0.7361 Intermediate Similarity NPC288084
0.7297 Intermediate Similarity NPC127546
0.7297 Intermediate Similarity NPC57625
0.7297 Intermediate Similarity NPC173637
0.7297 Intermediate Similarity NPC317489
0.7297 Intermediate Similarity NPC223424
0.7297 Intermediate Similarity NPC600591
0.7284 Intermediate Similarity NPC156869
0.7273 Intermediate Similarity NPC609478
0.725 Intermediate Similarity NPC29958
0.716 Intermediate Similarity NPC471748
0.716 Intermediate Similarity NPC39834
0.7143 Intermediate Similarity NPC182121
0.6974 Remote Similarity NPC265530
0.6933 Remote Similarity NPC111929
0.6933 Remote Similarity NPC320283
0.6933 Remote Similarity NPC41121
0.6923 Remote Similarity NPC175107
0.6842 Remote Similarity NPC476772
0.6829 Remote Similarity NPC139320
0.6795 Remote Similarity NPC42773
0.6795 Remote Similarity NPC138927
0.6795 Remote Similarity NPC45522
0.679 Remote Similarity NPC254855
0.679 Remote Similarity NPC94610
0.6753 Remote Similarity NPC136042
0.6585 Remote Similarity NPC116864
0.6585 Remote Similarity NPC244776
0.6582 Remote Similarity NPC599850
0.6538 Remote Similarity NPC297987
0.6506 Remote Similarity NPC480463
0.65 Remote Similarity NPC219904
0.6471 Remote Similarity NPC605592
0.6463 Remote Similarity NPC170052
0.6463 Remote Similarity NPC135846
0.6456 Remote Similarity NPC488080
0.6456 Remote Similarity NPC169977
0.6447 Remote Similarity NPC276222
0.6447 Remote Similarity NPC274618
0.6447 Remote Similarity NPC118284
0.6447 Remote Similarity NPC608147
0.642 Remote Similarity NPC189913
0.641 Remote Similarity NPC289667
0.641 Remote Similarity NPC143851
0.6404 Remote Similarity NPC76831
0.6375 Remote Similarity NPC21100
0.6364 Remote Similarity NPC37668
0.6353 Remote Similarity NPC67326
0.6351 Remote Similarity NPC78697
0.6344 Remote Similarity NPC292019
0.6344 Remote Similarity NPC202908
0.6341 Remote Similarity NPC223747
0.6341 Remote Similarity NPC605784
0.6329 Remote Similarity NPC8573
0.6329 Remote Similarity NPC158674
0.6296 Remote Similarity NPC191306
0.6296 Remote Similarity NPC488071
0.6279 Remote Similarity NPC203259
0.6279 Remote Similarity NPC33054
0.6279 Remote Similarity NPC155877
0.6279 Remote Similarity NPC176740
0.6279 Remote Similarity NPC471725
0.6279 Remote Similarity NPC134532
0.6279 Remote Similarity NPC602582
0.625 Remote Similarity NPC84362
0.618 Remote Similarity NPC270448
0.6163 Remote Similarity NPC470405
0.6145 Remote Similarity NPC116458
0.6145 Remote Similarity NPC246943
0.6104 Remote Similarity NPC54802
0.6104 Remote Similarity NPC197304
0.6064 Remote Similarity NPC189564
0.6049 Remote Similarity NPC24043
0.6047 Remote Similarity NPC471079
0.6047 Remote Similarity NPC609888
0.6024 Remote Similarity NPC101026
0.6024 Remote Similarity NPC488077
0.6024 Remote Similarity NPC197285
0.6024 Remote Similarity NPC484158
0.6024 Remote Similarity NPC601710
0.6023 Remote Similarity NPC255157
0.6023 Remote Similarity NPC259896
0.6 Remote Similarity NPC219043
0.6 Remote Similarity NPC48984
0.5977 Remote Similarity NPC173582
0.5977 Remote Similarity NPC196127
0.5977 Remote Similarity NPC265885
0.5977 Remote Similarity NPC181465
0.5977 Remote Similarity NPC215710
0.5977 Remote Similarity NPC163242
0.5977 Remote Similarity NPC272068
0.5977 Remote Similarity NPC473438
0.5977 Remote Similarity NPC253788
0.5955 Remote Similarity NPC253521
0.5955 Remote Similarity NPC154741
0.5955 Remote Similarity NPC113836
0.5952 Remote Similarity NPC88023
0.5952 Remote Similarity NPC209023
0.5952 Remote Similarity NPC309025
0.5938 Remote Similarity NPC470712
0.5904 Remote Similarity NPC235260
0.5904 Remote Similarity NPC159579
0.5904 Remote Similarity NPC155763
0.587 Remote Similarity NPC135831
0.5862 Remote Similarity NPC258044
0.5862 Remote Similarity NPC217387
0.5854 Remote Similarity NPC52550
0.5854 Remote Similarity NPC349108
0.5843 Remote Similarity NPC129264
0.5833 Remote Similarity NPC224530
0.5816 Remote Similarity NPC470718
0.5814 Remote Similarity NPC95866
0.5789 Remote Similarity NPC203145
0.5778 Remote Similarity NPC61904
0.5778 Remote Similarity NPC470125
0.5778 Remote Similarity NPC296018
0.5778 Remote Similarity NPC488073
0.5778 Remote Similarity NPC153755
0.5765 Remote Similarity NPC206123
0.5747 Remote Similarity NPC251417
0.5745 Remote Similarity NPC223426
0.5732 Remote Similarity NPC282987
0.573 Remote Similarity NPC304741
0.5699 Remote Similarity NPC471669
0.5684 Remote Similarity NPC81042
0.5682 Remote Similarity NPC480466
0.5663 Remote Similarity NPC305811
0.5657 Remote Similarity NPC279473
0.5652 Remote Similarity NPC473327
0.5644 Remote Similarity NPC470713
0.5638 Remote Similarity NPC292929
0.561 Remote Similarity NPC112755
0.561 Remote Similarity NPC170675
0.561 Remote Similarity NPC254306
0.5579 Remote Similarity NPC602448
0.5542 Remote Similarity NPC156457
0.5542 Remote Similarity NPC277205
0.5542 Remote Similarity NPC37919
0.5542 Remote Similarity NPC609879
0.5532 Remote Similarity NPC476472
0.5532 Remote Similarity NPC294815
0.5532 Remote Similarity NPC85751
0.5532 Remote Similarity NPC16194
0.5532 Remote Similarity NPC19240
0.5532 Remote Similarity NPC220173
0.5521 Remote Similarity NPC214621
0.5521 Remote Similarity NPC34267
0.5517 Remote Similarity NPC488072
0.5517 Remote Similarity NPC476215
0.5517 Remote Similarity NPC355481
0.5506 Remote Similarity NPC476773
0.5476 Remote Similarity NPC271692
0.5476 Remote Similarity NPC603655
0.5465 Remote Similarity NPC21666
0.5435 Remote Similarity NPC64425
0.5429 Remote Similarity NPC192539
0.5422 Remote Similarity NPC261866
0.5422 Remote Similarity NPC249281
0.5412 Remote Similarity NPC138540
0.5376 Remote Similarity NPC297503
0.5357 Remote Similarity NPC189142
0.5357 Remote Similarity NPC77660
0.5349 Remote Similarity NPC481043
0.5349 Remote Similarity NPC129217
0.5326 Remote Similarity NPC35167
0.5319 Remote Similarity NPC122467

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC95159 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
0.6279 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