Natural Product: NPC480421

Natural Product IDNPC480421
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
XAHBZJSZQWWSCJ-BYGDYCSISA-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 XAHBZJSZQWWSCJ-BYGDYCSISA-N
Standard InCHI InChI=1S/C68H110O34/c1-25-37(75)41(79)44(82)56(94-25)98-49-32(73)21-90-55(46(49)84)97-48-26(2)95-58(47(85)50(48)99-60-52(86)67(88,23-69)24-93-60)100-51-39(77)31(72)20-91-59(51)102-61(87)68-15-14-62(3,4)16-28(68)27-10-11-35-64(7)17-29(70)53(63(5,6)34(64)12-13-65(35,8)66(27,9)18-36(68)74)101-57-45(83)42(80)40(78)33(96-57)22-92-54-43(81)38(76)30(71)19-89-54/h10,25-26,28-60,69-86,88H,11-24H2,1-9H3/t25-,26-,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-,55-,56-,57-,58-,59-,60-,64-,65+,66+,67+,68+/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@H]1[C@H](CO[C@H]([C@@H]1O)O[C@H]1[C@H](C)O[C@H]([C@@H]([C@@H]1O[C@H]1[C@@H]([C@@](CO)(CO1)O)O)O)O[C@@H]1[C@H]([C@@H](CO[C@H]1OC(=O)[C@]12CCC(C)(C)C[C@H]1C1=CC[C@@H]3[C@@]4(C)C[C@@H]([C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)C[C@H]2O)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)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1470.69 Volume:   1375.601
?
Van der Waals volume.
Dense:   1.069 LogP:   0.665
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.34
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.681
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   17.0 Rigid Bonds:   68.0
TPSA:   530.66
?
Topological Polar Surface Area.
H-Bond Acceptor:   34.0
H-Bond Donor:   19.0 Rings:   12.0
Heavy Atoms:   34.0

MedChem Properties

QED Drug-Likeness Score:   0.039 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.413 Fsp3:   0.956
MCE-18:   264.331
?
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:   0.669 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
?
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:   0.375 Promiscuous compounds:   0.31

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.176 MDCK Permeability:   -4.92
Pgp-inhibitor:   0.0 Pgp-substrate:   0.999
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):   0.943
20% Bioavailability (F20%):   0.642 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.06
Plasma Protein Binding (PPB):   63.057% Volume Distribution (VD):   -0.333
Fu: 18.813%
?
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:   0.0
HLM stability:   0.0
?
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):  -1.075 Half-life (T1/2):  4.478

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.738 Drug-induced Liver Injury (DILI):  0.963
AMES Toxicity:  0.996 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.005 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.745 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  0.145 RPMI-8226 Immunitoxicity:  0.713
A549 Cytotoxicity:  0.997 Hek293 Cytotoxicity:  0.793
BCF:   0.86
?
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:   3.364
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.93
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.874
?
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 = 2700.0 nM PMID[30931559]
NPT113 Cell line RAW264.7 Mus musculus Inhibition > 50.0 % 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 NPC480421 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
0.7969 Intermediate Similarity NPC142151
0.7863 Intermediate Similarity NPC480422
0.7786 Intermediate Similarity NPC51099
0.7778 Intermediate Similarity NPC480418
0.771 Intermediate Similarity NPC480417
0.7692 Intermediate Similarity NPC267694
0.7674 Intermediate Similarity NPC144644
0.7674 Intermediate Similarity NPC170407
0.7444 Intermediate Similarity NPC68767
0.7405 Intermediate Similarity NPC37860
0.7364 Intermediate Similarity NPC13998
0.7259 Intermediate Similarity NPC153673
0.7185 Intermediate Similarity NPC102505
0.7185 Intermediate Similarity NPC293031
0.7185 Intermediate Similarity NPC488514
0.7143 Intermediate Similarity NPC309223
0.7101 Intermediate Similarity NPC275225
0.7054 Intermediate Similarity NPC480423
0.7007 Intermediate Similarity NPC110385
0.675 Remote Similarity NPC480420
0.6692 Remote Similarity NPC85154
0.6519 Remote Similarity NPC237191
0.6493 Remote Similarity NPC471577
0.6479 Remote Similarity NPC8524
0.6471 Remote Similarity NPC286457
0.6434 Remote Similarity NPC33012
0.6397 Remote Similarity NPC473386
0.635 Remote Similarity NPC473452
0.6212 Remote Similarity NPC815
0.6197 Remote Similarity NPC224381
0.6197 Remote Similarity NPC220160
0.6187 Remote Similarity NPC471580
0.6103 Remote Similarity NPC480419
0.6094 Remote Similarity NPC164389
0.6074 Remote Similarity NPC123522
0.6071 Remote Similarity NPC475514
0.604 Remote Similarity NPC489208
0.6038 Remote Similarity NPC472270
0.6038 Remote Similarity NPC112492
0.6026 Remote Similarity NPC485563
0.6015 Remote Similarity NPC104137
0.6015 Remote Similarity NPC26626
0.585 Remote Similarity NPC489209
0.5849 Remote Similarity NPC23020
0.5846 Remote Similarity NPC488526
0.5833 Remote Similarity NPC475584
0.5833 Remote Similarity NPC475152
0.5806 Remote Similarity NPC475394
0.5793 Remote Similarity NPC70809
0.5683 Remote Similarity NPC475899
0.568 Remote Similarity NPC488513
0.5674 Remote Similarity NPC488560
0.5646 Remote Similarity NPC482010
0.5639 Remote Similarity NPC488517
0.5594 Remote Similarity NPC21691
0.5591 Remote Similarity NPC475208
0.5548 Remote Similarity NPC236638
0.5548 Remote Similarity NPC294453
0.5517 Remote Similarity NPC470876
0.551 Remote Similarity NPC302543
0.5478 Remote Similarity NPC472268
0.5465 Remote Similarity NPC476113
0.5442 Remote Similarity NPC202828
0.5442 Remote Similarity NPC119592
0.5417 Remote Similarity NPC4749
0.5414 Remote Similarity NPC297950
0.5316 Remote Similarity NPC484831
0.5316 Remote Similarity NPC484830
0.5315 Remote Similarity NPC123199
0.5312 Remote Similarity NPC484829
0.5302 Remote Similarity NPC33068
0.5291 Remote Similarity NPC475527
0.528 Remote Similarity NPC475892
0.528 Remote Similarity NPC233223
0.528 Remote Similarity NPC183816
0.528 Remote Similarity NPC43589
0.5278 Remote Similarity NPC475160
0.5278 Remote Similarity NPC283417
0.5278 Remote Similarity NPC200049
0.5278 Remote Similarity NPC473714
0.5259 Remote Similarity NPC232237
0.5244 Remote Similarity NPC311178
0.5241 Remote Similarity NPC472269
0.5235 Remote Similarity NPC305981
0.5235 Remote Similarity NPC481081
0.5223 Remote Similarity NPC475177
0.5211 Remote Similarity NPC60557
0.5211 Remote Similarity NPC67857
0.5208 Remote Similarity NPC475209
0.52 Remote Similarity NPC261506
0.52 Remote Similarity NPC4328
0.5192 Remote Similarity NPC478822
0.5175 Remote Similarity NPC79643
0.517 Remote Similarity NPC476068
0.5168 Remote Similarity NPC293330
0.5154 Remote Similarity NPC1046
0.5118 Remote Similarity NPC322904
0.5113 Remote Similarity NPC173583
0.5109 Remote Similarity NPC105800
0.5105 Remote Similarity NPC76972
0.5105 Remote Similarity NPC469782
0.5105 Remote Similarity NPC204414
0.5103 Remote Similarity NPC135904
0.5101 Remote Similarity NPC41061
0.5101 Remote Similarity NPC227551
0.5099 Remote Similarity NPC298034
0.5099 Remote Similarity NPC71065
0.5098 Remote Similarity NPC250247
0.5077 Remote Similarity NPC238935
0.5071 Remote Similarity NPC481079
0.5068 Remote Similarity NPC57484
0.5065 Remote Similarity NPC478825
0.5063 Remote Similarity NPC475368
0.5061 Remote Similarity NPC300655
0.5061 Remote Similarity NPC196874
0.5036 Remote Similarity NPC305267
0.5035 Remote Similarity NPC295823
0.5035 Remote Similarity NPC174720
0.5035 Remote Similarity NPC475467
0.5035 Remote Similarity NPC69811
0.5034 Remote Similarity NPC473645
0.503 Remote Similarity NPC222951

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC480421 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