Natural Product: NPC525586

Natural Product IDNPC525586
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (2~{S},3~{R},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[2-(hydroxymethyl)phenoxy]tetrahydropyran-3,4,5-triol
IUPAC Name (2~{S},3~{R},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[2-(hydroxymethyl)phenoxy]tetrahydropyran-3,4,5-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 NGFMICBWJRZIBI-JZRPKSSGSA-N
Standard InCHI InChI=1S/C13H18O7/c14-5-7-3-1-2-4-8(7)19-13-12(18)11(17)10(16)9(6-15)20-13/h1-4,9-18H,5-6H2/t9-,10-,11-,12+,13+/m0/s1
SMILES OCC1=CC=CC=C1O[C@@H]1O[C@@H](CO)[C@H](O)[C@H](O)[C@H]1O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   286.11 Volume:   269.914
?
Van der Waals volume.
Dense:   1.06 LogP:   -0.302
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.149
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.292
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   12.0
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:   0.45 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.407 Fsp3:   0.538
MCE-18:   45.5
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.319 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.034
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.038
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.357 Promiscuous compounds:   0.008

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.393 MDCK Permeability:   -5.18
Pgp-inhibitor:   0.0 Pgp-substrate:   0.025
PAMPA:   0.961
?
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):   0.935
20% Bioavailability (F20%):   0.711 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   0.932

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.788 MRP1:   0.102
Plasma Protein Binding (PPB):   47.28% Volume Distribution (VD):   -0.41
Fu: 54.739%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.95
OATP1B3 inhibitor:   0.989 BCRP inhibitor:   0.031
BSEP inhibitor:   0.01

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.048
HLM stability:   0.001
?
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):  3.937 Half-life (T1/2):  1.749

ADMET: Toxicity

hERG Blockers:  0.015 hERG Blockers (10um):  0.171
Human Hepatotoxicity (H-HT):  0.561 Drug-induced Liver Injury (DILI):  0.301
AMES Toxicity:  0.822 Rat Oral Acute Toxicity:  0.027
Maximum Recommended Daily Dose:  0.015 Skin Sensitization:  0.989
Carcinogencity:  0.272 Eye Corrosion:  0.002
Eye Irritation:  0.819 Respiratory Toxicity:  0.031
Drug-induced Neurotoxicity:  0.052 Ototoxicity:  0.726
Hematotoxicity:  0.257 Drug-induced Nephrotoxicity:  0.554
Genotoxicity:  0.292 RPMI-8226 Immunitoxicity:  0.073
A549 Cytotoxicity:  0.121 Hek293 Cytotoxicity:  0.075
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:   2.236
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.639
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.727
?
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
NPO6424 Populus sieboldii Species Salicaceae Eukaryota n.a. n.a. n.a. PMID[16933880]
NPO14695 Populus davidiana Species Salicaceae Eukaryota stem bark n.a. n.a. PMID[16989539]
NPO19792 Populus tomentosa Species Salicaceae Eukaryota n.a. n.a. n.a. PMID[22860454]
NPO15986 Alangium chinense Species Cornaceae Eukaryota Roots n.a. n.a. PMID[23734721]
NPO64070 Salix songorica Genus Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30043 Populus beijingensis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO51124 Populus alba var.pyramdalis Genus Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10408 Populus adenopoda Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15986 Alangium chinense Species Cornaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19201 Populus alba Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10685 Salix daphnoides Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO58274 Populus canadensis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6424 Populus sieboldii Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3277 Salix alba Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14692 Salix babylonica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO56679 Populus spp. Genus Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4080 Salix purpurea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO51627 Salix spp. Genus Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16844 Populus lasiocarpa Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14068 Viburnum prunifolium Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO49404 Salix herbacea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30268 Populus xiaohei Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22941 Populus ussuriensis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19792 Populus tomentosa Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10537 Populus pseudo-simonii Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO61864 Populus nigra var.thevestina Genus Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5187 Populus koreana Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14847 Populus hopeiensis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14695 Populus davidiana Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15420 Populus cathayana Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5187 Populus koreana Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10408 Populus adenopoda Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30268 Populus xiaohei Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16844 Populus lasiocarpa Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14847 Populus hopeiensis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14692 Salix babylonica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15986 Alangium chinense Species Cornaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14695 Populus davidiana Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22941 Populus ussuriensis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14068 Viburnum prunifolium Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30043 Populus beijingensis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19792 Populus tomentosa Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10537 Populus pseudo-simonii Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19201 Populus alba Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4080 Salix purpurea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15420 Populus cathayana Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15986 Alangium chinense Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10537 Populus pseudo-simonii Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15420 Populus cathayana Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14068 Viburnum prunifolium Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19792 Populus tomentosa Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14847 Populus hopeiensis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22941 Populus ussuriensis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4080 Salix purpurea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16844 Populus lasiocarpa Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10408 Populus adenopoda Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19201 Populus alba Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14692 Salix babylonica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5187 Populus koreana Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14695 Populus davidiana Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14692 Salix babylonica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19792 Populus tomentosa Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4080 Salix purpurea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14068 Viburnum prunifolium Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19792 Populus tomentosa Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6424 Populus sieboldii Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3277 Salix alba Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4080 Salix purpurea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14068 Viburnum prunifolium Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14695 Populus davidiana Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15986 Alangium chinense Species Cornaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10685 Salix daphnoides Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19201 Populus alba Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22941 Populus ussuriensis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14692 Salix babylonica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16844 Populus lasiocarpa Species Salicaceae 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 NPC525586 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 NPC226712
0.75 Intermediate Similarity NPC608788
0.7045 Intermediate Similarity NPC228907
0.6731 Remote Similarity NPC40377
0.6667 Remote Similarity NPC269242
0.6538 Remote Similarity NPC166168
0.6316 Remote Similarity NPC34456
0.6275 Remote Similarity NPC299144
0.6226 Remote Similarity NPC166040
0.6207 Remote Similarity NPC146540
0.6207 Remote Similarity NPC269421
0.6122 Remote Similarity NPC212729
0.6122 Remote Similarity NPC604498
0.6 Remote Similarity NPC610808
0.5882 Remote Similarity NPC294470
0.5769 Remote Similarity NPC9248
0.5763 Remote Similarity NPC31081
0.5714 Remote Similarity NPC218685
0.5686 Remote Similarity NPC217854
0.566 Remote Similarity NPC60589
0.566 Remote Similarity NPC469708
0.566 Remote Similarity NPC609376
0.5614 Remote Similarity NPC606892
0.5593 Remote Similarity NPC245219
0.5556 Remote Similarity NPC200092
0.5556 Remote Similarity NPC302989
0.5538 Remote Similarity NPC101116
0.5536 Remote Similarity NPC9912
0.5517 Remote Similarity NPC164599
0.549 Remote Similarity NPC276195
0.549 Remote Similarity NPC142319
0.5472 Remote Similarity NPC25817
0.5472 Remote Similarity NPC152722
0.5455 Remote Similarity NPC69513
0.5455 Remote Similarity NPC80098
0.5397 Remote Similarity NPC600107
0.5373 Remote Similarity NPC217950
0.5357 Remote Similarity NPC48863
0.5357 Remote Similarity NPC251981
0.5357 Remote Similarity NPC13745
0.5345 Remote Similarity NPC472024
0.5345 Remote Similarity NPC270849
0.5345 Remote Similarity NPC602619
0.5333 Remote Similarity NPC222455
0.5323 Remote Similarity NPC134260
0.5283 Remote Similarity NPC153149
0.5263 Remote Similarity NPC215833
0.5254 Remote Similarity NPC26653
0.5254 Remote Similarity NPC80600
0.5254 Remote Similarity NPC210478
0.5224 Remote Similarity NPC212099
0.5217 Remote Similarity NPC166180
0.5172 Remote Similarity NPC49074
0.5167 Remote Similarity NPC248355
0.5167 Remote Similarity NPC479029
0.5156 Remote Similarity NPC87696
0.5152 Remote Similarity NPC278329
0.5152 Remote Similarity NPC92054
0.5152 Remote Similarity NPC605700
0.5143 Remote Similarity NPC292443
0.5094 Remote Similarity NPC484157
0.5091 Remote Similarity NPC604439
0.5088 Remote Similarity NPC214454
0.5088 Remote Similarity NPC95292
0.5085 Remote Similarity NPC251102
0.5085 Remote Similarity NPC162093
0.5085 Remote Similarity NPC479028
0.5085 Remote Similarity NPC485268
0.5085 Remote Similarity NPC205054
0.5085 Remote Similarity NPC210298
0.5085 Remote Similarity NPC23084
0.5085 Remote Similarity NPC479031
0.5085 Remote Similarity NPC19470
0.5085 Remote Similarity NPC604356
0.5082 Remote Similarity NPC106025
0.5082 Remote Similarity NPC55040

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC525586 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
1.0 High Similarity NPD1091 Pre-clinical

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