Natural Product: NPC471424

Natural Product IDNPC471424
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
NMMYHIHPRVYSQO-SZPRDVAZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2442978
PubChem CID 46930487
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 NMMYHIHPRVYSQO-SZPRDVAZSA-N
Standard InCHI InChI=1S/C64H106O30/c1-25-36(70)41(75)44(78)53(85-25)92-49-39(73)29(21-67)88-57(51(49)94-52-47(81)48(26(68)22-82-52)91-54-45(79)42(76)37(71)27(19-65)86-54)89-30-23-83-56(50(40(30)74)93-55-46(80)43(77)38(72)28(20-66)87-55)90-35-11-12-60(6)31(59(35,4)5)9-13-61(7)32(60)10-14-64-33-17-58(2,3)15-16-63(33,24-84-64)34(69)18-62(61,64)8/h25-57,65-81H,9-24H2,1-8H3/t25-,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+,52-,53-,54-,55-,56-,57-,60-,61+,62-,63+,64-/m0/s1
SMILES OC[C@H]1O[C@@H](O[C@H]2[C@@H](OC[C@@H]([C@@H]2O)O[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O[C@@H]2OC[C@H]([C@@H]([C@H]2O)O[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O)O)O[C@@H]2O[C@@H](C)[C@@H]([C@H]([C@H]2O)O)O)O)O[C@H]2CC[C@]3([C@H](C2(C)C)CC[C@@]2([C@@H]3CC[C@]34[C@@]2(C)C[C@H]([C@@]2([C@H]4CC(C)(C)CC2)CO3)O)C)C)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1354.68 Volume:   1276.529
?
Van der Waals volume.
Dense:   1.061 LogP:   -0.791
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.291
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.353
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The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   65.0
TPSA:   463.9
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Topological Polar Surface Area.
H-Bond Acceptor:   30.0
H-Bond Donor:   17.0 Rings:   12.0
Heavy Atoms:   30.0

MedChem Properties

QED Drug-Likeness Score:   0.069 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.81 Fsp3:   1.0
MCE-18:   344.531
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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:   0.781 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:   0.001
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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:   0.449 Promiscuous compounds:   0.008

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.399 MDCK Permeability:   -4.753
Pgp-inhibitor:   0.0 Pgp-substrate:   0.814
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):   0.954
20% Bioavailability (F20%):   0.011 30% Bioavailability (F30%):   0.998
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.0
Plasma Protein Binding (PPB):   51.016% Volume Distribution (VD):   -0.352
Fu: 27.568%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.004
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:   1.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.008
HLM stability:   0.002
?
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):  -1.733 Half-life (T1/2):  5.422

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.004
Human Hepatotoxicity (H-HT):  0.517 Drug-induced Liver Injury (DILI):  0.831
AMES Toxicity:  0.962 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:  0.474 Drug-induced Nephrotoxicity:  0.989
Genotoxicity:  0.016 RPMI-8226 Immunitoxicity:  0.297
A549 Cytotoxicity:  0.56 Hek293 Cytotoxicity:  0.321
BCF:   1.122
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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:   3.51
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.022
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.912
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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
NPO32586 ardisia gigantifolia stapf. Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[24095094]
NPO32586 ardisia gigantifolia stapf. Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT181 Cell line Bel-7402 Homo sapiens Activity = 59.94 % PMID[18959441]
NPT181 Cell line Bel-7402 Homo sapiens Activity = 40.86 % PMID[14510607]
NPT180 Cell line HCT-8 Homo sapiens IC50 = 10060.0 nM PubChem BioAssay data set
NPT181 Cell line Bel-7402 Homo sapiens IC50 = 7830.0 nM DOI[10.6019/CHEMBL1201861]
NPT81 Cell line A549 Homo sapiens IC50 = 8150.0 nM DailyMed

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 NPC471424 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
0.9115 High Similarity NPC471626
0.8957 High Similarity NPC471428
0.8829 High Similarity NPC471425
0.875 High Similarity NPC189575
0.819 Intermediate Similarity NPC471429
0.8136 Intermediate Similarity NPC471426
0.812 Intermediate Similarity NPC231566
0.8051 Intermediate Similarity NPC106701
0.8 Intermediate Similarity NPC253611
0.8 Intermediate Similarity NPC488782
0.7983 Intermediate Similarity NPC471427
0.7845 Intermediate Similarity NPC205129
0.7778 Intermediate Similarity NPC262567
0.7593 Intermediate Similarity NPC18724
0.7561 Intermediate Similarity NPC471431
0.7456 Intermediate Similarity NPC77717
0.7436 Intermediate Similarity NPC209798
0.7304 Intermediate Similarity NPC267238
0.7241 Intermediate Similarity NPC40716
0.6957 Remote Similarity NPC171741
0.6903 Remote Similarity NPC224003
0.6842 Remote Similarity NPC158051
0.6833 Remote Similarity NPC138219
0.6833 Remote Similarity NPC475234
0.6807 Remote Similarity NPC148593
0.6772 Remote Similarity NPC22709
0.6748 Remote Similarity NPC126753
0.6719 Remote Similarity NPC471430
0.6667 Remote Similarity NPC471373
0.6639 Remote Similarity NPC473688
0.6475 Remote Similarity NPC184805
0.6364 Remote Similarity NPC158367
0.6311 Remote Similarity NPC470623
0.6303 Remote Similarity NPC323231
0.629 Remote Similarity NPC475630
0.624 Remote Similarity NPC471375
0.619 Remote Similarity NPC51579
0.6179 Remote Similarity NPC207693
0.6129 Remote Similarity NPC157571
0.6032 Remote Similarity NPC273189
0.576 Remote Similarity NPC119628
0.5758 Remote Similarity NPC470622
0.5736 Remote Similarity NPC471374
0.5714 Remote Similarity NPC66513
0.5285 Remote Similarity NPC285253
0.5197 Remote Similarity NPC157474
0.5154 Remote Similarity NPC476305
0.5152 Remote Similarity NPC87393
0.5079 Remote Similarity NPC110494

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471424 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