Natural Product: NPC471024

Natural Product IDNPC471024
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Purgin Ii
IUPAC Name n.a.
Synonyms Purgin II
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2336636
PubChem CID 71720744
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003918] Saccharolipids

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 KBURMVDNPRIDQL-RBNNPITQSA-N
Standard InCHI InChI=1S/C140H224O54/c1-15-21-25-27-31-39-55-67-95(147)183-127-125(193-132-107(159)102(154)99(151)89(73-141)175-132)117(189-134-111(163)120(115(81(11)168-134)185-129(165)77(7)19-5)180-97(149)71-69-85-57-47-43-48-58-85)83(13)171-139(127)187-113-79(9)167-131(108(160)105(113)157)191-122-103(155)100(152)90(74-142)176-137(122)173-87(61-45-23-17-3)63-51-37-33-29-35-41-53-65-93(145)179-119-92(76-144)178-133(109(161)106(119)158)194-126-118(190-135-112(164)121(116(82(12)169-135)186-130(166)78(8)20-6)181-98(150)72-70-86-59-49-44-50-60-86)84(14)172-140(128(126)184-96(148)68-56-40-32-28-26-22-16-2)188-114-80(10)170-136-124(110(114)162)182-94(146)66-54-42-36-30-34-38-52-64-88(62-46-24-18-4)174-138-123(192-136)104(156)101(153)91(75-143)177-138/h43-44,47-50,57-60,69-72,77-84,87-92,99-128,131-144,151-164H,15-42,45-46,51-56,61-68,73-76H2,1-14H3/b71-69+,72-70+/t77-,78-,79-,80-,81-,82-,83-,84-,87-,88-,89+,90+,91+,92+,99+,100+,101+,102-,103-,104-,105-,106+,107+,108+,109+,110+,111+,112+,113-,114-,115-,116-,117-,118-,119+,120-,121-,122+,123+,124+,125+,126+,127+,128+,131-,132-,133-,134-,135-,136-,137+,138+,139-,140-/m0/s1
SMILES CCCCCCCCCC(=O)O[C@H]1[C@@H](O[C@H]([C@@H]([C@H]1O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)OC(=O)CCCCCCCCC[C@@H](O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1OC(=O)CCCCCCCCC)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)OC(=O)/C=C/c1ccccc1)OC(=O)[C@H](CC)C)O)O)CCCCC)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)OC(=O)/C=C/c1ccccc1)OC(=O)[C@H](CC)C)C)O[C@H]1[C@H](C)O[C@@H]2[C@@H]([C@@H]1O)OC(=O)CCCCCCCCC[C@@H](O[C@H]1[C@H](O2)[C@@H](O)[C@@H]([C@H](O1)CO)O)CCCCC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   2769.48 Volume:   2751.249
?
Van der Waals volume.
Dense:   1.007 LogP:   9.936
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   7.395
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -7.387
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   76.0 Rigid Bonds:   98.0
TPSA:   759.14
?
Topological Polar Surface Area.
H-Bond Acceptor:   54.0
H-Bond Donor:   18.0 Rings:   13.0
Heavy Atoms:   54.0

MedChem Properties

QED Drug-Likeness Score:   0.013 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   9.332 Fsp3:   0.829
MCE-18:   357.281
?
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:   1.0 Fluc inhibitor:   0.667
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.083
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.333
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.443 Promiscuous compounds:   0.213

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.744 MDCK Permeability:   -5.325
Pgp-inhibitor:   0.0 Pgp-substrate:   0.998
PAMPA:   0.999
?
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):   0.805
20% Bioavailability (F20%):   0.443 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.751
Plasma Protein Binding (PPB):   95.908% Volume Distribution (VD):   -0.346
Fu: 3.182%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.069

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:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.001
?
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):  -0.937 Half-life (T1/2):  8.334

ADMET: Toxicity

hERG Blockers:  0.026 hERG Blockers (10um):  0.011
Human Hepatotoxicity (H-HT):  0.647 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  0.741 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.769 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.926
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.919
BCF:   -0.232
?
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:   6.375
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   8.438
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.985
?
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
NPO19106 Ipomoea purga Species Convolvulaceae Eukaryota n.a. aerial part n.a. PMID[21446661]
NPO19106 Ipomoea purga Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[23273047]
NPO19106 Ipomoea purga Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19106 Ipomoea purga Species Convolvulaceae 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
NPT668 Individual protein P-glycoprotein 1 Homo sapiens FC > 2140.6 n.a. PMID[17877337]
NPT668 Individual protein P-glycoprotein 1 Homo sapiens FC > 1687.5 n.a. PMID[17877337]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT83 Cell line MCF7 Homo sapiens FC > 73.4 n.a. PMID[17877337]
NPT83 Cell line MCF7 Homo sapiens IC50 > 25.0 ug.mL-1 PMID[24913558]

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 NPC471024 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
0.94 High Similarity NPC471025
0.9167 High Similarity NPC147032
0.8173 Intermediate Similarity NPC77651
0.8113 Intermediate Similarity NPC10883
0.7778 Intermediate Similarity NPC290276
0.7407 Intermediate Similarity NPC35338
0.7407 Intermediate Similarity NPC204214
0.7407 Intermediate Similarity NPC92283
0.7339 Intermediate Similarity NPC28069
0.7297 Intermediate Similarity NPC10121
0.7297 Intermediate Similarity NPC198918
0.7248 Intermediate Similarity NPC63404
0.7 Intermediate Similarity NPC124878
0.7 Intermediate Similarity NPC231888
0.6636 Remote Similarity NPC184915
0.6636 Remote Similarity NPC224953
0.6514 Remote Similarity NPC44782
0.6481 Remote Similarity NPC183888
0.6481 Remote Similarity NPC259294
0.6381 Remote Similarity NPC109887
0.6364 Remote Similarity NPC471026
0.633 Remote Similarity NPC126685
0.6296 Remote Similarity NPC478726
0.6239 Remote Similarity NPC162925
0.6126 Remote Similarity NPC472200
0.6055 Remote Similarity NPC472204
0.6055 Remote Similarity NPC119583
0.6 Remote Similarity NPC483170
0.5981 Remote Similarity NPC477326
0.5946 Remote Similarity NPC115013
0.5909 Remote Similarity NPC307400
0.5909 Remote Similarity NPC27289
0.5888 Remote Similarity NPC89843
0.5888 Remote Similarity NPC477331
0.5872 Remote Similarity NPC478725
0.5849 Remote Similarity NPC87153
0.5833 Remote Similarity NPC477344
0.5833 Remote Similarity NPC600446
0.5833 Remote Similarity NPC605013
0.5818 Remote Similarity NPC478723
0.5818 Remote Similarity NPC478724
0.5818 Remote Similarity NPC477319
0.5804 Remote Similarity NPC169345
0.5766 Remote Similarity NPC143421
0.5741 Remote Similarity NPC478734
0.5702 Remote Similarity NPC123204
0.5676 Remote Similarity NPC472205
0.5664 Remote Similarity NPC290012
0.5664 Remote Similarity NPC477317
0.5664 Remote Similarity NPC477318
0.5648 Remote Similarity NPC604005
0.5648 Remote Similarity NPC605014
0.5636 Remote Similarity NPC478733
0.5575 Remote Similarity NPC238264
0.5575 Remote Similarity NPC477345
0.5556 Remote Similarity NPC478727
0.5556 Remote Similarity NPC22742
0.5556 Remote Similarity NPC477346
0.5536 Remote Similarity NPC297768
0.5512 Remote Similarity NPC600940
0.5481 Remote Similarity NPC478729
0.5476 Remote Similarity NPC600721
0.5476 Remote Similarity NPC605872
0.547 Remote Similarity NPC478728
0.5446 Remote Similarity NPC146992
0.5446 Remote Similarity NPC85759
0.5446 Remote Similarity NPC478722
0.5446 Remote Similarity NPC267592
0.544 Remote Similarity NPC600672
0.5421 Remote Similarity NPC477330
0.5413 Remote Similarity NPC113745
0.5413 Remote Similarity NPC477320
0.5413 Remote Similarity NPC477323
0.5413 Remote Similarity NPC477325
0.5413 Remote Similarity NPC609436
0.5391 Remote Similarity NPC610997
0.537 Remote Similarity NPC281563
0.537 Remote Similarity NPC477329
0.536 Remote Similarity NPC611287
0.5351 Remote Similarity NPC294748
0.5333 Remote Similarity NPC475241
0.5315 Remote Similarity NPC477332
0.5278 Remote Similarity NPC477328
0.5259 Remote Similarity NPC238056
0.5197 Remote Similarity NPC610996
0.5185 Remote Similarity NPC146380
0.5093 Remote Similarity NPC477350
0.5047 Remote Similarity NPC606819

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471024 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