Natural Product: NPC532734

Natural Product IDNPC532734
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~{R},5~{R},6~{S})-2-[(2~{R},3~{R},4~{S},5~{R},6~{R})-5-hydroxy-6-(hydroxymethyl)-2-[[(1~{S},2~{S},4~{S},6~{S},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-6-hydroxy-7,9,13-trimethyl-6-[(2~{R},4~{R},5~{S})-4-methyl-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-tetrahydrofuran-2-yl]-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-en-16-yl]oxy]-4-[(2~{S},3~{R},4~{S},5~{R})-3,4,5-trihydroxytetrahydropyran-2-yl]oxy-tetrahydropyran-3-yl]oxy-6-methyl-tetrahydropyran-3,4,5-triol
IUPAC Name (2~{S},3~{R},4~{R},5~{R},6~{S})-2-[(2~{R},3~{R},4~{S},5~{R},6~{R})-5-hydroxy-6-(hydroxymethyl)-2-[[(1~{S},2~{S},4~{S},6~{S},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-6-hydroxy-7,9,13-trimethyl-6-[(2~{R},4~{R},5~{S})-4-methyl-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-tetrahydrofuran-2-yl]-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-en-16-yl]oxy]-4-[(2~{S},3~{R},4~{S},5~{R})-3,4,5-trihydroxytetrahydropyran-2-yl]oxy-tetrahydropyran-3-yl]oxy-6-methyl-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 RKECRWWERANOKJ-ASLGXAEJSA-N
Standard InCHI InChI=1S/C50H80O23/c1-18-12-30(69-43(18)72-46-40(62)37(59)34(56)28(15-51)67-46)50(63)19(2)31-27(73-50)14-25-23-7-6-21-13-22(8-10-48(21,4)24(23)9-11-49(25,31)5)66-47-42(71-45-39(61)36(58)32(54)20(3)65-45)41(35(57)29(16-52)68-47)70-44-38(60)33(55)26(53)17-64-44/h6,18-20,22-47,51-63H,7-17H2,1-5H3/t18-,19+,20+,22+,23-,24+,25+,26-,27+,28-,29-,30-,31+,32+,33+,34-,35-,36-,37+,38-,39-,40-,41+,42-,43+,44+,45+,46+,47-,48+,49+,50+/m1/s1
SMILES C[C@@H]1C[C@H]([C@@]2(O)O[C@H]3C[C@H]4[C@@H]5CC=C6C[C@@H](O[C@@H]7O[C@H](CO)[C@@H](O)[C@H](O[C@@H]8OC[C@@H](O)[C@H](O)[C@H]8O)[C@H]7O[C@@H]7O[C@@H](C)[C@H](O)[C@@H](O)[C@H]7O)CC[C@]6(C)[C@H]5CC[C@]4(C)[C@H]3[C@@H]2C)O[C@H]1O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1048.51 Volume:   987.33
?
Van der Waals volume.
Dense:   1.062 LogP:   1.249
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.065
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.116
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The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   53.0
TPSA:   355.29
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Topological Polar Surface Area.
H-Bond Acceptor:   23.0
H-Bond Donor:   13.0 Rings:   10.0
Heavy Atoms:   23.0

MedChem Properties

QED Drug-Likeness Score:   0.092 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.931 Fsp3:   0.96
MCE-18:   195.735
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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:   0 PAINS Alert:   0
Colloidal aggregators:   0.576 Fluc inhibitor:   0.0
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.41 Promiscuous compounds:   0.04

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.552 MDCK Permeability:   -5.145
Pgp-inhibitor:   0.0 Pgp-substrate:   0.988
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):   0.04
20% Bioavailability (F20%):   0.005 30% Bioavailability (F30%):   0.98
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.0
Plasma Protein Binding (PPB):   36.504% Volume Distribution (VD):   -0.478
Fu: 46.335%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.145
BSEP inhibitor:   0.0

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:   0.002
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):  -0.447 Half-life (T1/2):  4.274

ADMET: Toxicity

hERG Blockers:  0.007 hERG Blockers (10um):  0.028
Human Hepatotoxicity (H-HT):  0.263 Drug-induced Liver Injury (DILI):  0.901
AMES Toxicity:  0.947 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.004 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.495 Drug-induced Nephrotoxicity:  0.846
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.346
A549 Cytotoxicity:  0.805 Hek293 Cytotoxicity:  0.57
BCF:   1.441
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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:   3.315
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.47
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.763
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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
NPO8266 Solanum anguivi Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8266 Solanum anguivi Species Solanaceae 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 NPC532734 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
0.7727 Intermediate Similarity NPC218571
0.7727 Intermediate Similarity NPC487615
0.7273 Intermediate Similarity NPC102016
0.7273 Intermediate Similarity NPC95051
0.6525 Remote Similarity NPC249265
0.6356 Remote Similarity NPC309278
0.6348 Remote Similarity NPC300557
0.6293 Remote Similarity NPC150057
0.6293 Remote Similarity NPC147753
0.6174 Remote Similarity NPC602423
0.6102 Remote Similarity NPC73243
0.6102 Remote Similarity NPC244086
0.6102 Remote Similarity NPC84956
0.6087 Remote Similarity NPC98696
0.6 Remote Similarity NPC247037
0.5806 Remote Similarity NPC23808
0.5806 Remote Similarity NPC87998
0.5798 Remote Similarity NPC48886
0.5798 Remote Similarity NPC94881
0.5794 Remote Similarity NPC232054
0.5691 Remote Similarity NPC475333
0.5691 Remote Similarity NPC224098
0.5691 Remote Similarity NPC208383
0.562 Remote Similarity NPC475182
0.5603 Remote Similarity NPC94272
0.5538 Remote Similarity NPC480556
0.5512 Remote Similarity NPC256983
0.5469 Remote Similarity NPC31896
0.5447 Remote Similarity NPC98018
0.5447 Remote Similarity NPC284104
0.5447 Remote Similarity NPC103616
0.5397 Remote Similarity NPC194207
0.5397 Remote Similarity NPC22779
0.5366 Remote Similarity NPC480555
0.5366 Remote Similarity NPC150372
0.5338 Remote Similarity NPC477808
0.5285 Remote Similarity NPC6806
0.5271 Remote Similarity NPC477811
0.525 Remote Similarity NPC305423
0.525 Remote Similarity NPC113044
0.525 Remote Similarity NPC283829
0.525 Remote Similarity NPC161676
0.5207 Remote Similarity NPC475351
0.5188 Remote Similarity NPC248202
0.5185 Remote Similarity NPC210569
0.5161 Remote Similarity NPC51172
0.5161 Remote Similarity NPC49032
0.5154 Remote Similarity NPC84111
0.5154 Remote Similarity NPC287483
0.5154 Remote Similarity NPC470865
0.5154 Remote Similarity NPC480553
0.5122 Remote Similarity NPC470433
0.5122 Remote Similarity NPC46190
0.5122 Remote Similarity NPC171073
0.5115 Remote Similarity NPC308140
0.5081 Remote Similarity NPC248746
0.5081 Remote Similarity NPC122819
0.5072 Remote Similarity NPC244431
0.5072 Remote Similarity NPC305771
0.5072 Remote Similarity NPC263359
0.5072 Remote Similarity NPC94072
0.5072 Remote Similarity NPC169816
0.5041 Remote Similarity NPC486388
0.504 Remote Similarity NPC42171
0.5039 Remote Similarity NPC51520
0.5039 Remote Similarity NPC303069
0.5036 Remote Similarity NPC208832

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC532734 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
0.6293 Remote Similarity NPD8450 Suspended
0.5081 Remote Similarity NPD8449 Approved

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