Natural Product: NPC581057

Natural Product IDNPC581057
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
(2~{R},3~{R},4~{R},5~{R},6~{S})-2-[[(2~{R},3~{R},4~{S},5~{R},6~{S})-6-[(2~{R},3~{R},4~{R},5~{R},6~{R})-4,5-dihydroxy-6-[(1~{R},2~{S},4~{S},5'~{S},6~{R},7~{S},8~{R},9~{S},12~{S},13~{S},16~{S},18~{R})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-tetrahydropyran]-16-yl]oxy-2-[[(2~{R},3~{R},4~{S},5~{R},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxymethyl]tetrahydropyran-3-yl]oxy-3,4,5-trihydroxy-tetrahydropyran-2-yl]methoxy]-6-methyl-tetrahydropyran-3,4,5-triol
IUPAC Name (2~{R},3~{R},4~{R},5~{R},6~{S})-2-[[(2~{R},3~{R},4~{S},5~{R},6~{S})-6-[(2~{R},3~{R},4~{R},5~{R},6~{R})-4,5-dihydroxy-6-[(1~{R},2~{S},4~{S},5'~{S},6~{R},7~{S},8~{R},9~{S},12~{S},13~{S},16~{S},18~{R})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-tetrahydropyran]-16-yl]oxy-2-[[(2~{R},3~{R},4~{S},5~{R},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxymethyl]tetrahydropyran-3-yl]oxy-3,4,5-trihydroxy-tetrahydropyran-2-yl]methoxy]-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 SJWPDTJDCFSPLW-BFCHINECSA-N
Standard InCHI InChI=1S/C51H84O22/c1-20-8-13-51(66-17-20)21(2)32-28(73-51)15-27-25-7-6-23-14-24(9-11-49(23,4)26(25)10-12-50(27,32)5)68-47-43(63)39(59)44(31(71-47)19-65-46-41(61)37(57)34(54)29(16-52)69-46)72-48-42(62)38(58)35(55)30(70-48)18-64-45-40(60)36(56)33(53)22(3)67-45/h20-48,52-63H,6-19H2,1-5H3/t20-,21-,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-,51+/m0/s1
SMILES C[C@H]1CC[C@@]2(OC1)O[C@H]1C[C@H]3[C@@H]4CC[C@@H]5C[C@@H](O[C@@H]6O[C@H](CO[C@@H]7O[C@H](CO)[C@H](O)[C@H](O)[C@H]7O)[C@H](O[C@@H]7O[C@H](CO[C@@H]8O[C@@H](C)[C@H](O)[C@@H](O)[C@H]8O)[C@H](O)[C@H](O)[C@H]7O)[C@H](O)[C@H]6O)CC[C@]5(C)[C@H]4CC[C@]3(C)[C@H]1[C@@H]2C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1048.55 Volume:   998.472
?
Van der Waals volume.
Dense:   1.05 LogP:   1.513
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.111
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.375
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The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   54.0
TPSA:   335.06
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Topological Polar Surface Area.
H-Bond Acceptor:   22.0
H-Bond Donor:   12.0 Rings:   10.0
Heavy Atoms:   22.0

MedChem Properties

QED Drug-Likeness Score:   0.101 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.159 Fsp3:   1.0
MCE-18:   261.333
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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:   0.663 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.022
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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:   0.371 Promiscuous compounds:   0.012

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.431 MDCK Permeability:   -5.068
Pgp-inhibitor:   0.0 Pgp-substrate:   0.99
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):   0.036
20% Bioavailability (F20%):   0.988 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.532
Plasma Protein Binding (PPB):   52.538% Volume Distribution (VD):   -0.366
Fu: 33.512%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.002
BSEP inhibitor:   0.001

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.47 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.63
HLM stability:   0.019
?
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):  0.158 Half-life (T1/2):  2.403

ADMET: Toxicity

hERG Blockers:  0.007 hERG Blockers (10um):  0.019
Human Hepatotoxicity (H-HT):  0.498 Drug-induced Liver Injury (DILI):  0.965
AMES Toxicity:  0.995 Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.004 Skin Sensitization:  1.0
Carcinogencity:  0.053 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.001 Ototoxicity:  0.999
Hematotoxicity:  0.778 Drug-induced Nephrotoxicity:  0.917
Genotoxicity:  0.002 RPMI-8226 Immunitoxicity:  0.527
A549 Cytotoxicity:  0.999 Hek293 Cytotoxicity:  0.984
BCF:   1.825
?
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:   3.471
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.551
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.923
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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
NPO17292 Asparagus racemosus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17292 Asparagus racemosus Species Asparagaceae 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 NPC581057 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
0.9186 High Similarity NPC107188
0.7778 Intermediate Similarity NPC325828
0.7708 Intermediate Similarity NPC160426
0.7553 Intermediate Similarity NPC211354
0.7391 Intermediate Similarity NPC177834
0.7255 Intermediate Similarity NPC128572
0.7234 Intermediate Similarity NPC477451
0.7216 Intermediate Similarity NPC107962
0.7158 Intermediate Similarity NPC250393
0.7143 Intermediate Similarity NPC6295
0.7129 Intermediate Similarity NPC475643
0.7128 Intermediate Similarity NPC234352
0.7021 Intermediate Similarity NPC297348
0.7021 Intermediate Similarity NPC249204
0.7021 Intermediate Similarity NPC48339
0.7021 Intermediate Similarity NPC141769
0.7021 Intermediate Similarity NPC477547
0.6907 Remote Similarity NPC206003
0.6907 Remote Similarity NPC473610
0.6857 Remote Similarity NPC97700
0.6857 Remote Similarity NPC30856
0.6837 Remote Similarity NPC19400
0.6809 Remote Similarity NPC485594
0.6789 Remote Similarity NPC83137
0.6765 Remote Similarity NPC475351
0.6699 Remote Similarity NPC202898
0.6698 Remote Similarity NPC184617
0.66 Remote Similarity NPC264101
0.6577 Remote Similarity NPC132080
0.6396 Remote Similarity NPC470864
0.6364 Remote Similarity NPC475625
0.6364 Remote Similarity NPC116756
0.6306 Remote Similarity NPC232037
0.6214 Remote Similarity NPC215408
0.6154 Remote Similarity NPC125324
0.6154 Remote Similarity NPC470432
0.6154 Remote Similarity NPC230507
0.6154 Remote Similarity NPC485595
0.6139 Remote Similarity NPC222731
0.6121 Remote Similarity NPC470866
0.6111 Remote Similarity NPC92890
0.6095 Remote Similarity NPC195297
0.6055 Remote Similarity NPC471464
0.6055 Remote Similarity NPC51172
0.6055 Remote Similarity NPC6806
0.6055 Remote Similarity NPC49032
0.5969 Remote Similarity NPC481189
0.5941 Remote Similarity NPC294686
0.5923 Remote Similarity NPC329727
0.59 Remote Similarity NPC181845
0.5862 Remote Similarity NPC233433
0.5859 Remote Similarity NPC329807
0.578 Remote Similarity NPC473601
0.5766 Remote Similarity NPC300557
0.5758 Remote Similarity NPC24960
0.5752 Remote Similarity NPC115165
0.5752 Remote Similarity NPC475319
0.5741 Remote Similarity NPC113044
0.5741 Remote Similarity NPC283829
0.5741 Remote Similarity NPC14704
0.5741 Remote Similarity NPC161676
0.5714 Remote Similarity NPC480555
0.5714 Remote Similarity NPC150372
0.5676 Remote Similarity NPC477809
0.5669 Remote Similarity NPC481190
0.5657 Remote Similarity NPC473774
0.5657 Remote Similarity NPC481419
0.5657 Remote Similarity NPC481417
0.5656 Remote Similarity NPC220836
0.5641 Remote Similarity NPC476112
0.5641 Remote Similarity NPC307534
0.5586 Remote Similarity NPC602423
0.5517 Remote Similarity NPC309278
0.5472 Remote Similarity NPC121453
0.547 Remote Similarity NPC194207
0.547 Remote Similarity NPC22779
0.5462 Remote Similarity NPC480553
0.5455 Remote Similarity NPC277715
0.5446 Remote Similarity NPC470433
0.5446 Remote Similarity NPC46190
0.5446 Remote Similarity NPC171073
0.5431 Remote Similarity NPC269297
0.5431 Remote Similarity NPC222202
0.541 Remote Similarity NPC94086
0.541 Remote Similarity NPC473817
0.5385 Remote Similarity NPC475333
0.5385 Remote Similarity NPC473518
0.5385 Remote Similarity NPC224098
0.5385 Remote Similarity NPC208383
0.5378 Remote Similarity NPC470862
0.5364 Remote Similarity NPC141433
0.5354 Remote Similarity NPC144790
0.5354 Remote Similarity NPC149400
0.5347 Remote Similarity NPC481420
0.5347 Remote Similarity NPC481421
0.5339 Remote Similarity NPC232611
0.5299 Remote Similarity NPC329820
0.5294 Remote Similarity NPC172838
0.5294 Remote Similarity NPC480554
0.5278 Remote Similarity NPC54619
0.5267 Remote Similarity NPC330026
0.5246 Remote Similarity NPC232054
0.5242 Remote Similarity NPC480556
0.5207 Remote Similarity NPC477811
0.5189 Remote Similarity NPC291203
0.5189 Remote Similarity NPC217205
0.5172 Remote Similarity NPC151134
0.5167 Remote Similarity NPC108072
0.5138 Remote Similarity NPC306131
0.5138 Remote Similarity NPC200802
0.5126 Remote Similarity NPC32361
0.5094 Remote Similarity NPC137004
0.5093 Remote Similarity NPC474399
0.5089 Remote Similarity NPC70204
0.5079 Remote Similarity NPC224314
0.5047 Remote Similarity NPC131693
0.5047 Remote Similarity NPC475436
0.5042 Remote Similarity NPC470863
0.5041 Remote Similarity NPC31896

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC581057 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
0.7778 Intermediate Similarity NPD8171 Phase 2
0.6634 Remote Similarity NPD8170 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