Natural Product: NPC252201

Natural Product IDNPC252201
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SVRJGKAZQHHOSZ-UOCKATJYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101068307
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 SVRJGKAZQHHOSZ-UOCKATJYSA-N
Standard InCHI InChI=1S/C23H22O14/c1-7(24)34-6-14-17(30)19(32)20(33)23(36-14)37-22-18(31)15-10(26)4-9(25)5-13(15)35-21(22)8-2-11(27)16(29)12(28)3-8/h2-5,14,17,19-20,23,25-30,32-33H,6H2,1H3/t14-,17+,19+,20-,23+/m1/s1
SMILES CC(=O)OC[C@@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)Oc1c(=O)c2c(cc(cc2oc1c1cc(c(c(c1)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   522.1 Volume:   471.473
?
Van der Waals volume.
Dense:   1.107 LogP:   0.659
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.834
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.353
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   25.0
TPSA:   236.81
?
Topological Polar Surface Area.
 H-Bond Acceptor:   14.0
H-Bond Donor:   8.0 Rings:   4.0
Heavy Atoms:   14.0

MedChem Properties

QED Drug-Likeness Score:   0.159 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.21 Fsp3:   0.304
MCE-18:   96.667
?
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:   Accepted BMS Rule:   1
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.653 Fluc inhibitor:   0.193
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.858
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.685
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.079 Promiscuous compounds:   0.88

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.337 MDCK Permeability:   -5.104
Pgp-inhibitor:   0.0 Pgp-substrate:   0.662
PAMPA:   0.999
?
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):   0.004
20% Bioavailability (F20%):   0.306 30% Bioavailability (F30%):   0.988
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.069
Plasma Protein Binding (PPB):   84.477% Volume Distribution (VD):   -0.076
Fu: 13.92%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.974
OATP1B3 inhibitor:   0.992 BCRP inhibitor:   0.85
BSEP inhibitor:   0.413

ADMET: Metabolism

CYP1A2-inhibitor:   0.01 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.052
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.01
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.998
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.989
?
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):  2.802 Half-life (T1/2):  3.438

ADMET: Toxicity

hERG Blockers:  0.008 hERG Blockers (10um):  0.479
Human Hepatotoxicity (H-HT):  0.289 Drug-induced Liver Injury (DILI):  0.821
AMES Toxicity:  0.725 Rat Oral Acute Toxicity:  0.097
Maximum Recommended Daily Dose:  0.325 Skin Sensitization:  1.0
Carcinogencity:  0.082 Eye Corrosion:  0.001
Eye Irritation:  0.96 Respiratory Toxicity:  0.047
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.924
Hematotoxicity:  0.013 Drug-induced Nephrotoxicity:  0.009
Genotoxicity:  0.973 RPMI-8226 Immunitoxicity:  0.011
A549 Cytotoxicity:  0.935 Hek293 Cytotoxicity:  0.22
BCF:   0.489
?
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:   3.116
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.507
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.887
?
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
NPO7485 Nymphaea odorata Species Nymphaeaceae Eukaryota n.a. n.a. n.a. PMID[12713413]
NPO14224 Haloxylon recurvum Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[16274989]
NPO14224 Haloxylon recurvum Species Chenopodiaceae Eukaryota n.a. whole plant n.a. PMID[16651755]
NPO7986 Austrocedrus chilensis Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[25420758]
NPO1458 Burkholderia gladioli Species Burkholderiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO6569 Ranunculus fluitans Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14224 Haloxylon recurvum Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7485 Nymphaea odorata Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7986 Austrocedrus chilensis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6569 Ranunculus fluitans Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO164 Senecio carthamoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7485 Nymphaea odorata Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1580 Heliotropium ternatum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1458 Burkholderia gladioli Species Burkholderiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO9697 Araliopsis soyauxii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14224 Haloxylon recurvum Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1332 Inula salicifolia 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 NPC252201 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
0.8816 High Similarity NPC116864
0.8816 High Similarity NPC244776
0.825 Intermediate Similarity NPC39834
0.8125 Intermediate Similarity NPC609888
0.7867 Intermediate Similarity NPC135599
0.7867 Intermediate Similarity NPC73855
0.7867 Intermediate Similarity NPC113968
0.7867 Intermediate Similarity NPC328940
0.7867 Intermediate Similarity NPC277174
0.7867 Intermediate Similarity NPC606877
0.7738 Intermediate Similarity NPC153755
0.7532 Intermediate Similarity NPC19388
0.7532 Intermediate Similarity NPC240431
0.7532 Intermediate Similarity NPC55786
0.7386 Intermediate Similarity NPC471669
0.7375 Intermediate Similarity NPC182121
0.7294 Intermediate Similarity NPC203259
0.7294 Intermediate Similarity NPC33054
0.7294 Intermediate Similarity NPC176740
0.7294 Intermediate Similarity NPC471725
0.7294 Intermediate Similarity NPC134532
0.7294 Intermediate Similarity NPC602582
0.7176 Intermediate Similarity NPC67326
0.7159 Intermediate Similarity NPC37668
0.7143 Intermediate Similarity NPC34531
0.7093 Intermediate Similarity NPC156869
0.7033 Intermediate Similarity NPC223426
0.6977 Remote Similarity NPC173582
0.6977 Remote Similarity NPC265885
0.6977 Remote Similarity NPC181465
0.6977 Remote Similarity NPC215710
0.6977 Remote Similarity NPC473438
0.6977 Remote Similarity NPC253788
0.6966 Remote Similarity NPC270448
0.6957 Remote Similarity NPC81042
0.6875 Remote Similarity NPC127546
0.6875 Remote Similarity NPC57625
0.6875 Remote Similarity NPC173637
0.6875 Remote Similarity NPC317489
0.6875 Remote Similarity NPC223424
0.6875 Remote Similarity NPC600591
0.686 Remote Similarity NPC471079
0.6813 Remote Similarity NPC85751
0.6813 Remote Similarity NPC19240
0.6778 Remote Similarity NPC473327
0.6774 Remote Similarity NPC214621
0.6774 Remote Similarity NPC34267
0.675 Remote Similarity NPC476771
0.6747 Remote Similarity NPC175107
0.6667 Remote Similarity NPC189913
0.6667 Remote Similarity NPC476772
0.6629 Remote Similarity NPC129264
0.6585 Remote Similarity NPC145038
0.6585 Remote Similarity NPC56077
0.6585 Remote Similarity NPC281131
0.6585 Remote Similarity NPC253662
0.6585 Remote Similarity NPC265530
0.6585 Remote Similarity NPC179950
0.6585 Remote Similarity NPC88789
0.6585 Remote Similarity NPC491374
0.6556 Remote Similarity NPC154741
0.6543 Remote Similarity NPC111929
0.6543 Remote Similarity NPC320283
0.6543 Remote Similarity NPC41121
0.6452 Remote Similarity NPC476472
0.6452 Remote Similarity NPC294815
0.6452 Remote Similarity NPC16194
0.6429 Remote Similarity NPC138927
0.6392 Remote Similarity NPC292019
0.6392 Remote Similarity NPC202908
0.6392 Remote Similarity NPC477895
0.6386 Remote Similarity NPC64305
0.6374 Remote Similarity NPC470125
0.6374 Remote Similarity NPC296018
0.6364 Remote Similarity NPC139571
0.6353 Remote Similarity NPC219904
0.6327 Remote Similarity NPC217520
0.6296 Remote Similarity NPC276222
0.6296 Remote Similarity NPC274618
0.6296 Remote Similarity NPC118284
0.6296 Remote Similarity NPC608147
0.6279 Remote Similarity NPC484158
0.6265 Remote Similarity NPC77672
0.6265 Remote Similarity NPC133671
0.6265 Remote Similarity NPC135391
0.6265 Remote Similarity NPC78263
0.6265 Remote Similarity NPC250069
0.6235 Remote Similarity NPC472459
0.622 Remote Similarity NPC67037
0.622 Remote Similarity NPC255615
0.6207 Remote Similarity NPC209023
0.619 Remote Similarity NPC158674
0.6163 Remote Similarity NPC159579
0.6163 Remote Similarity NPC60735
0.6163 Remote Similarity NPC26230
0.6122 Remote Similarity NPC189564
0.6105 Remote Similarity NPC89127
0.6092 Remote Similarity NPC120099
0.6047 Remote Similarity NPC325555
0.6047 Remote Similarity NPC226304
0.6044 Remote Similarity NPC196127
0.6023 Remote Similarity NPC223747
0.5978 Remote Similarity NPC65563
0.5978 Remote Similarity NPC470949
0.5976 Remote Similarity NPC54802
0.5976 Remote Similarity NPC197304
0.5938 Remote Similarity NPC135831
0.5934 Remote Similarity NPC258044
0.5934 Remote Similarity NPC217387
0.5904 Remote Similarity NPC288084
0.5895 Remote Similarity NPC122467
0.5876 Remote Similarity NPC470445
0.587 Remote Similarity NPC471748
0.5851 Remote Similarity NPC126784
0.5851 Remote Similarity NPC241423
0.5851 Remote Similarity NPC488074
0.5816 Remote Similarity NPC470446
0.5806 Remote Similarity NPC605592
0.5778 Remote Similarity NPC203050
0.5778 Remote Similarity NPC225434
0.5761 Remote Similarity NPC187379
0.5761 Remote Similarity NPC29958
0.573 Remote Similarity NPC609478
0.57 Remote Similarity NPC121703
0.5684 Remote Similarity NPC488073
0.567 Remote Similarity NPC486577
0.566 Remote Similarity NPC488740
0.566 Remote Similarity NPC488736
0.566 Remote Similarity NPC488733
0.5644 Remote Similarity NPC470451
0.5625 Remote Similarity NPC12013
0.5625 Remote Similarity NPC11432
0.5625 Remote Similarity NPC477613
0.5618 Remote Similarity NPC235260
0.5618 Remote Similarity NPC155763
0.5618 Remote Similarity NPC129217
0.5612 Remote Similarity NPC470447
0.5607 Remote Similarity NPC480444
0.5604 Remote Similarity NPC355481
0.5591 Remote Similarity NPC139320
0.5579 Remote Similarity NPC473571
0.5579 Remote Similarity NPC110941
0.5579 Remote Similarity NPC186816
0.5568 Remote Similarity NPC52550
0.5568 Remote Similarity NPC349108
0.5556 Remote Similarity NPC488737
0.5556 Remote Similarity NPC85707
0.5556 Remote Similarity NPC36138
0.5556 Remote Similarity NPC470449
0.5545 Remote Similarity NPC203145
0.5543 Remote Similarity NPC95866
0.5514 Remote Similarity NPC156785
0.551 Remote Similarity NPC97119
0.5506 Remote Similarity NPC216496
0.55 Remote Similarity NPC470450
0.5484 Remote Similarity NPC254540
0.5472 Remote Similarity NPC488734
0.5472 Remote Similarity NPC488735
0.5472 Remote Similarity NPC488739
0.5472 Remote Similarity NPC488732
0.5472 Remote Similarity NPC488738
0.5464 Remote Similarity NPC470443
0.5455 Remote Similarity NPC76831
0.5455 Remote Similarity NPC477629
0.5446 Remote Similarity NPC470455
0.5437 Remote Similarity NPC173837
0.5421 Remote Similarity NPC480445
0.5417 Remote Similarity NPC35167
0.5417 Remote Similarity NPC144097
0.5413 Remote Similarity NPC241781
0.54 Remote Similarity NPC221342
0.54 Remote Similarity NPC476470
0.5393 Remote Similarity NPC305811
0.5393 Remote Similarity NPC271692
0.5385 Remote Similarity NPC303694
0.5385 Remote Similarity NPC224530
0.5376 Remote Similarity NPC254855
0.5376 Remote Similarity NPC94610
0.5376 Remote Similarity NPC477848
0.5368 Remote Similarity NPC227508
0.5354 Remote Similarity NPC603079
0.5347 Remote Similarity NPC602448
0.534 Remote Similarity NPC470416
0.5333 Remote Similarity NPC277532
0.5312 Remote Similarity NPC155877
0.53 Remote Similarity NPC473073
0.5294 Remote Similarity NPC96605
0.5294 Remote Similarity NPC280642
0.5275 Remote Similarity NPC48093
0.5269 Remote Similarity NPC476215
0.5269 Remote Similarity NPC53587
0.5258 Remote Similarity NPC255157
0.5258 Remote Similarity NPC259896
0.5253 Remote Similarity NPC104883
0.5253 Remote Similarity NPC488679
0.5248 Remote Similarity NPC292929
0.5248 Remote Similarity NPC287889
0.5243 Remote Similarity NPC89052
0.5229 Remote Similarity NPC162394
0.5229 Remote Similarity NPC474522

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC252201 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
0.7294 Intermediate Similarity NPD6797 Phase 2
0.5455 Remote Similarity NPD7251 Phase 2
0.5096 Remote Similarity NPD7808 Phase 3

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