Natural Product: NPC480418

Natural Product IDNPC480418
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
PFSKILNTQIYQKJ-XWHBEEMPSA-N
IUPAC Name n.a.
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 PFSKILNTQIYQKJ-XWHBEEMPSA-N
Standard InCHI InChI=1S/C62H100O29/c1-25-44(87-50-41(74)36(69)30(66)20-81-50)45(88-54-47(77)62(79,23-63)24-84-54)43(76)52(85-25)89-46-37(70)31(67)21-82-53(46)91-55(78)61-15-13-56(2,3)17-27(61)26-9-10-34-58(6)18-28(64)48(57(4,5)33(58)11-12-60(34,8)59(26,7)14-16-61)90-51-42(75)39(72)38(71)32(86-51)22-83-49-40(73)35(68)29(65)19-80-49/h9,25,27-54,63-77,79H,10-24H2,1-8H3/t25-,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-,52-,53-,54-,58-,59+,60+,61-,62+/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@@H](CO[C@H]1OC(=O)[C@@]12CCC(C)(C)C[C@H]2C2=CC[C@@H]3[C@@]4(C)C[C@@H]([C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]2(C)CC1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@H](CO2)O)O)O)O1)O)O)O)O)O)O)O)O[C@H]1[C@@H]([C@@](CO)(CO1)O)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1308.64 Volume:   1236.43
?
Van der Waals volume.
Dense:   1.058 LogP:   1.141
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.744
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.217
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   62.0
TPSA:   451.51
?
Topological Polar Surface Area.
H-Bond Acceptor:   29.0
H-Bond Donor:   16.0 Rings:   11.0
Heavy Atoms:   29.0

MedChem Properties

QED Drug-Likeness Score:   0.045 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.661 Fsp3:   0.952
MCE-18:   238.843
?
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:   0.689 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.29 Promiscuous compounds:   0.301

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.814 MDCK Permeability:   -5.035
Pgp-inhibitor:   0.0 Pgp-substrate:   0.981
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):   0.688
20% Bioavailability (F20%):   0.613 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.027
Plasma Protein Binding (PPB):   69.152% Volume Distribution (VD):   -0.344
Fu: 15.584%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
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:   0.092
HLM stability:   0.034
?
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):  -0.637 Half-life (T1/2):  3.781

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.002
Human Hepatotoxicity (H-HT):  0.727 Drug-induced Liver Injury (DILI):  0.757
AMES Toxicity:  0.987 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.009 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.503 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  0.055 RPMI-8226 Immunitoxicity:  0.592
A549 Cytotoxicity:  0.982 Hek293 Cytotoxicity:  0.612
BCF:   1.463
?
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:   3.638
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.372
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.41
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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
NPO28688 Aster tataricus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[30931559]
NPO28688 Aster tataricus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28688 Aster tataricus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28688 Aster tataricus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28688 Aster tataricus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28688 Aster tataricus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28688 Aster tataricus 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
NPT113 Cell line RAW264.7 Mus musculus IC50 > 50000.0 nM PMID[30931559]

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 NPC480418 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
0.8803 High Similarity NPC480417
0.7903 Intermediate Similarity NPC480422
0.7778 Intermediate Similarity NPC480421
0.7692 Intermediate Similarity NPC480419
0.6748 Remote Similarity NPC475899
0.664 Remote Similarity NPC480423
0.6515 Remote Similarity NPC142151
0.6434 Remote Similarity NPC473645
0.6391 Remote Similarity NPC267694
0.6387 Remote Similarity NPC63159
0.637 Remote Similarity NPC51099
0.6316 Remote Similarity NPC70809
0.6293 Remote Similarity NPC480420
0.6269 Remote Similarity NPC224381
0.6241 Remote Similarity NPC144644
0.6241 Remote Similarity NPC170407
0.619 Remote Similarity NPC60557
0.619 Remote Similarity NPC67857
0.6172 Remote Similarity NPC123199
0.6165 Remote Similarity NPC236638
0.6165 Remote Similarity NPC294453
0.6119 Remote Similarity NPC37860
0.6063 Remote Similarity NPC76972
0.6063 Remote Similarity NPC469782
0.6063 Remote Similarity NPC204414
0.6061 Remote Similarity NPC13998
0.6058 Remote Similarity NPC68767
0.6048 Remote Similarity NPC481079
0.6047 Remote Similarity NPC135904
0.6045 Remote Similarity NPC202828
0.6045 Remote Similarity NPC119592
0.6032 Remote Similarity NPC815
0.6016 Remote Similarity NPC79643
0.6 Remote Similarity NPC295823
0.6 Remote Similarity NPC174720
0.6 Remote Similarity NPC475467
0.5985 Remote Similarity NPC57484
0.5966 Remote Similarity NPC295371
0.5957 Remote Similarity NPC478822
0.5942 Remote Similarity NPC293031
0.5931 Remote Similarity NPC472268
0.5899 Remote Similarity NPC153673
0.5896 Remote Similarity NPC41061
0.5896 Remote Similarity NPC227551
0.5873 Remote Similarity NPC241909
0.5862 Remote Similarity NPC297950
0.5809 Remote Similarity NPC305981
0.5809 Remote Similarity NPC481081
0.5786 Remote Similarity NPC110385
0.5775 Remote Similarity NPC275225
0.5766 Remote Similarity NPC261506
0.5766 Remote Similarity NPC4328
0.5764 Remote Similarity NPC489208
0.5763 Remote Similarity NPC48499
0.5714 Remote Similarity NPC488560
0.5704 Remote Similarity NPC286457
0.5703 Remote Similarity NPC104137
0.5703 Remote Similarity NPC26626
0.5703 Remote Similarity NPC481078
0.5672 Remote Similarity NPC481080
0.5656 Remote Similarity NPC469946
0.5652 Remote Similarity NPC298034
0.5652 Remote Similarity NPC71065
0.5645 Remote Similarity NPC488526
0.5643 Remote Similarity NPC250247
0.562 Remote Similarity NPC293330
0.561 Remote Similarity NPC112352
0.5588 Remote Similarity NPC473452
0.5563 Remote Similarity NPC489209
0.5556 Remote Similarity NPC488517
0.5548 Remote Similarity NPC472269
0.5537 Remote Similarity NPC139894
0.5528 Remote Similarity NPC473343
0.5493 Remote Similarity NPC102505
0.5493 Remote Similarity NPC488514
0.5492 Remote Similarity NPC150400
0.5486 Remote Similarity NPC477464
0.5462 Remote Similarity NPC31838
0.5462 Remote Similarity NPC187290
0.5441 Remote Similarity NPC487505
0.5441 Remote Similarity NPC85154
0.5433 Remote Similarity NPC297263
0.5429 Remote Similarity NPC309223
0.5426 Remote Similarity NPC301449
0.5426 Remote Similarity NPC601290
0.5373 Remote Similarity NPC165204
0.5366 Remote Similarity NPC480424
0.5357 Remote Similarity NPC477463
0.5352 Remote Similarity NPC482010
0.5338 Remote Similarity NPC300419
0.5333 Remote Similarity NPC155410
0.5329 Remote Similarity NPC45606
0.5324 Remote Similarity NPC258617
0.5317 Remote Similarity NPC104071
0.531 Remote Similarity NPC8524
0.5299 Remote Similarity NPC123522
0.5299 Remote Similarity NPC192600
0.5294 Remote Similarity NPC475160
0.5294 Remote Similarity NPC100639
0.5294 Remote Similarity NPC470218
0.5294 Remote Similarity NPC473714
0.5289 Remote Similarity NPC29069
0.5286 Remote Similarity NPC43550
0.5276 Remote Similarity NPC102439
0.5274 Remote Similarity NPC33012
0.5252 Remote Similarity NPC110633
0.5224 Remote Similarity NPC475287
0.5197 Remote Similarity NPC30735
0.5194 Remote Similarity NPC475504
0.5182 Remote Similarity NPC191827
0.5177 Remote Similarity NPC65105
0.5157 Remote Similarity NPC482013
0.5156 Remote Similarity NPC164389
0.5156 Remote Similarity NPC232237
0.5156 Remote Similarity NPC473459
0.5139 Remote Similarity NPC220160
0.5122 Remote Similarity NPC179434
0.5105 Remote Similarity NPC482012
0.5097 Remote Similarity NPC220838
0.5077 Remote Similarity NPC222580
0.5071 Remote Similarity NPC476068
0.5067 Remote Similarity NPC475368
0.5039 Remote Similarity NPC263756
0.5039 Remote Similarity NPC251768
0.5039 Remote Similarity NPC46665
0.5039 Remote Similarity NPC480475
0.5038 Remote Similarity NPC488515
0.5036 Remote Similarity NPC471577
0.5034 Remote Similarity NPC478823
0.5034 Remote Similarity NPC478824
0.5033 Remote Similarity NPC475177
0.5033 Remote Similarity NPC484831
0.5033 Remote Similarity NPC484830

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC480418 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
NPD

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