Natural Product: NPC480419

Natural Product IDNPC480419
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
OQQNUYZCCRCGQK-PHWDVUOMSA-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 OQQNUYZCCRCGQK-PHWDVUOMSA-N
Standard InCHI InChI=1S/C57H92O24/c1-24-44(78-35-17-27(58)29(60)20-72-35)40(67)43(70)48(76-24)79-45-37(64)31(62)22-74-50(45)81-51(71)57-15-13-52(2,3)18-26(57)25-9-10-34-54(6)19-28(59)46(53(4,5)33(54)11-12-56(34,8)55(25,7)14-16-57)80-49-42(69)39(66)38(65)32(77-49)23-75-47-41(68)36(63)30(61)21-73-47/h9,24,26-50,58-70H,10-23H2,1-8H3/t24-,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-,54-,55+,56+,57-/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)O[C@H]1C[C@H]([C@@H](CO1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1160.6 Volume:   1114.556
?
Van der Waals volume.
Dense:   1.041 LogP:   1.408
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.997
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.432
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   57.0
TPSA:   372.36
?
Topological Polar Surface Area.
H-Bond Acceptor:   24.0
H-Bond Donor:   13.0 Rings:   10.0
Heavy Atoms:   24.0

MedChem Properties

QED Drug-Likeness Score:   0.065 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.185 Fsp3:   0.947
MCE-18:   213.622
?
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:   0.793 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.008
?
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:   0.246 Promiscuous compounds:   0.098

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.452 MDCK Permeability:   -5.095
Pgp-inhibitor:   0.0 Pgp-substrate:   0.993
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):   0.769
20% Bioavailability (F20%):   0.869 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.031
Plasma Protein Binding (PPB):   73.396% Volume Distribution (VD):   -0.336
Fu: 13.584%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
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:   0.052
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.944
HLM stability:   0.318
?
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):  -0.511 Half-life (T1/2):  4.113

ADMET: Toxicity

hERG Blockers:  0.002 hERG Blockers (10um):  0.009
Human Hepatotoxicity (H-HT):  0.751 Drug-induced Liver Injury (DILI):  0.964
AMES Toxicity:  0.974 Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.004 Skin Sensitization:  1.0
Carcinogencity:  0.015 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.458 Drug-induced Nephrotoxicity:  0.998
Genotoxicity:  0.432 RPMI-8226 Immunitoxicity:  0.527
A549 Cytotoxicity:  0.96 Hek293 Cytotoxicity:  0.502
BCF:   1.807
?
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:   3.808
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.414
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.602
?
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 NPC480419 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
0.8624 High Similarity NPC480423
0.7692 Intermediate Similarity NPC480418
0.6797 Remote Similarity NPC480417
0.6641 Remote Similarity NPC224381
0.6577 Remote Similarity NPC480420
0.6562 Remote Similarity NPC70809
0.6429 Remote Similarity NPC13998
0.6417 Remote Similarity NPC815
0.6379 Remote Similarity NPC63159
0.6349 Remote Similarity NPC57484
0.6311 Remote Similarity NPC60557
0.6311 Remote Similarity NPC67857
0.6194 Remote Similarity NPC480422
0.6179 Remote Similarity NPC76972
0.6179 Remote Similarity NPC469782
0.6179 Remote Similarity NPC204414
0.616 Remote Similarity NPC135904
0.6154 Remote Similarity NPC236638
0.6154 Remote Similarity NPC294453
0.6116 Remote Similarity NPC295823
0.6116 Remote Similarity NPC174720
0.6116 Remote Similarity NPC475467
0.6103 Remote Similarity NPC480421
0.6071 Remote Similarity NPC297950
0.6066 Remote Similarity NPC104137
0.6066 Remote Similarity NPC26626
0.6033 Remote Similarity NPC481079
0.6032 Remote Similarity NPC123199
0.6031 Remote Similarity NPC202828
0.6031 Remote Similarity NPC119592
0.6028 Remote Similarity NPC472268
0.5984 Remote Similarity NPC241909
0.5948 Remote Similarity NPC295371
0.5878 Remote Similarity NPC41061
0.5878 Remote Similarity NPC227551
0.5873 Remote Similarity NPC79643
0.5809 Remote Similarity NPC102505
0.5809 Remote Similarity NPC488514
0.5794 Remote Similarity NPC300419
0.5789 Remote Similarity NPC305981
0.575 Remote Similarity NPC488526
0.5746 Remote Similarity NPC261506
0.5746 Remote Similarity NPC309223
0.5746 Remote Similarity NPC4328
0.5746 Remote Similarity NPC144644
0.5746 Remote Similarity NPC170407
0.5739 Remote Similarity NPC48499
0.5714 Remote Similarity NPC112352
0.5703 Remote Similarity NPC475899
0.5692 Remote Similarity NPC488560
0.5672 Remote Similarity NPC481081
0.5649 Remote Similarity NPC85154
0.5649 Remote Similarity NPC481080
0.563 Remote Similarity NPC298034
0.563 Remote Similarity NPC71065
0.563 Remote Similarity NPC473343
0.563 Remote Similarity NPC37860
0.563 Remote Similarity NPC469946
0.5629 Remote Similarity NPC472269
0.562 Remote Similarity NPC250247
0.5597 Remote Similarity NPC293330
0.5593 Remote Similarity NPC480424
0.558 Remote Similarity NPC68767
0.5564 Remote Similarity NPC286457
0.5556 Remote Similarity NPC481078
0.5528 Remote Similarity NPC488517
0.5508 Remote Similarity NPC139894
0.5468 Remote Similarity NPC293031
0.5462 Remote Similarity NPC150400
0.5462 Remote Similarity NPC165204
0.5448 Remote Similarity NPC473452
0.5433 Remote Similarity NPC31838
0.542 Remote Similarity NPC155410
0.541 Remote Similarity NPC104071
0.5403 Remote Similarity NPC297263
0.5385 Remote Similarity NPC29069
0.5379 Remote Similarity NPC100639
0.5366 Remote Similarity NPC102439
0.5308 Remote Similarity NPC475287
0.5294 Remote Similarity NPC258617
0.5276 Remote Similarity NPC301449
0.5276 Remote Similarity NPC601290
0.5263 Remote Similarity NPC475160
0.5263 Remote Similarity NPC470218
0.5263 Remote Similarity NPC473714
0.5259 Remote Similarity NPC473386
0.5255 Remote Similarity NPC43550
0.5242 Remote Similarity NPC164389
0.5242 Remote Similarity NPC232237
0.5224 Remote Similarity NPC471577
0.5221 Remote Similarity NPC110633
0.5214 Remote Similarity NPC142151
0.5194 Remote Similarity NPC187290
0.5175 Remote Similarity NPC8524
0.5159 Remote Similarity NPC222580
0.5159 Remote Similarity NPC475504
0.5152 Remote Similarity NPC192600
0.5147 Remote Similarity NPC476068
0.5145 Remote Similarity NPC65105
0.5139 Remote Similarity NPC33012
0.512 Remote Similarity NPC480475
0.5118 Remote Similarity NPC488515
0.5116 Remote Similarity NPC96641
0.5116 Remote Similarity NPC163183
0.5106 Remote Similarity NPC478823
0.5106 Remote Similarity NPC220160
0.5106 Remote Similarity NPC267694
0.5105 Remote Similarity NPC153673
0.5105 Remote Similarity NPC51099
0.5102 Remote Similarity NPC489208
0.5083 Remote Similarity NPC179434
0.5079 Remote Similarity NPC235438
0.5072 Remote Similarity NPC471580
0.5072 Remote Similarity NPC470876
0.5037 Remote Similarity NPC191827
0.5036 Remote Similarity NPC237191

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC480419 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