Natural Product: NPC147032

Natural Product IDNPC147032
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Purgin I
IUPAC Name n.a.
Synonyms Purgin I
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2336642
PubChem CID 53355581
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 FQYZTZXSIFWAPT-NMRWSHIASA-N
Standard InCHI InChI=1S/C144H232O52/c1-17-23-27-29-31-33-39-45-61-73-99(149)185-131-129(195-136-111(161)106(156)105(155)95(79-145)179-136)121(191-138-116(166)124(120(88(14)172-138)188-134(168)82(8)22-6)182-101(151)77-75-91-63-53-49-54-64-91)89(15)175-143(131)189-117-85(11)171-135(112(162)109(117)159)193-125-107(157)103(153)83(9)169-139(125)177-93(67-51-25-19-3)69-57-43-37-35-41-47-59-71-97(147)181-123-96(80-146)180-137(113(163)110(123)160)196-130-122(192-141-127(184-102(152)78-76-92-65-55-50-56-66-92)114(164)118(86(12)173-141)187-133(167)81(7)21-5)90(16)176-144(132(130)186-100(150)74-62-46-40-34-32-30-28-24-18-2)190-119-87(13)174-142-128(115(119)165)183-98(148)72-60-48-42-36-38-44-58-70-94(68-52-26-20-4)178-140-126(194-142)108(158)104(154)84(10)170-140/h49-50,53-56,63-66,75-78,81-90,93-96,103-132,135-146,153-166H,17-48,51-52,57-62,67-74,79-80H2,1-16H3/b77-75+,78-76+/t81-,82-,83+,84+,85-,86-,87-,88-,89-,90-,93-,94-,95+,96+,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+,129+,130+,131+,132+,135-,136-,137-,138-,139-,140-,141-,142-,143-,144-/m0/s1
SMILES CCCCCCCCCCCC(=O)O[C@@H]1[C@@H]([C@H]([C@H](C)O[C@H]1O[C@H]1[C@H](C)O[C@H]([C@@H]([C@@H]1O)O)O[C@@H]1[C@H]([C@H]([C@@H](C)O[C@H]1O[C@@H](CCCCC)CCCCCCCCCC(=O)O[C@@H]1[C@@H](CO)O[C@H]([C@@H]([C@H]1O)O)O[C@@H]1[C@H]([C@H](C)O[C@H]([C@@H]1OC(=O)CCCCCCCCCCC)O[C@H]1[C@H](C)O[C@@H]2[C@@H]([C@@H]1O)OC(=O)CCCCCCCCC[C@H](CCCCC)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](C)O1)O)O)O2)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)OC(=O)[C@@H](C)CC)O)OC(=O)/C=C/c1ccccc1)O)O)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)OC(=O)[C@@H](C)CC)OC(=O)/C=C/c1ccccc1)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   2793.55 Volume:   2802.853
?
Van der Waals volume.
Dense:   0.997 LogP:   13.955
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   9.24
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -8.429
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   78.0 Rigid Bonds:   98.0
TPSA:   718.68
?
Topological Polar Surface Area.
H-Bond Acceptor:   52.0
H-Bond Donor:   16.0 Rings:   13.0
Heavy Atoms:   52.0

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:   9.358 Fsp3:   0.833
MCE-18:   355.818
?
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:   0.088
?
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:   0.042

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.733 MDCK Permeability:   -5.346
Pgp-inhibitor:   0.0 Pgp-substrate:   0.999
PAMPA:   0.995
?
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):   0.794
20% Bioavailability (F20%):   0.963 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.997
Plasma Protein Binding (PPB):   96.93% Volume Distribution (VD):   -0.145
Fu: 1.698%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.698

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:   0.003
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):  -0.518 Half-life (T1/2):  9.382

ADMET: Toxicity

hERG Blockers:  0.14 hERG Blockers (10um):  0.14
Human Hepatotoxicity (H-HT):  0.501 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  0.721 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:  0.883 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.968
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.989
BCF:   0.666
?
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:   7.737
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   9.382
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   7.949
?
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 = 4.7 n.a. PMID[23273047]
NPT668 Individual protein P-glycoprotein 1 Homo sapiens FC = 3.8 n.a. PMID[23273047]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT83 Cell line MCF7 Homo sapiens IC50 > 25.0 ug.mL-1 PMID[23273047]
NPT83 Cell line MCF7 Homo sapiens FC = 2.9 n.a. PMID[23273047]

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 NPC147032 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
0.9167 High Similarity NPC471024
0.8611 High Similarity NPC471025
0.8598 High Similarity NPC290276
0.8318 Intermediate Similarity NPC77651
0.8257 Intermediate Similarity NPC10883
0.8091 Intermediate Similarity NPC10121
0.8091 Intermediate Similarity NPC198918
0.7982 Intermediate Similarity NPC28069
0.7727 Intermediate Similarity NPC35338
0.7727 Intermediate Similarity NPC204214
0.7727 Intermediate Similarity NPC92283
0.7568 Intermediate Similarity NPC63404
0.7321 Intermediate Similarity NPC124878
0.7321 Intermediate Similarity NPC231888
0.6972 Remote Similarity NPC183888
0.6972 Remote Similarity NPC224953
0.6881 Remote Similarity NPC162925
0.6818 Remote Similarity NPC126685
0.6574 Remote Similarity NPC109887
0.6532 Remote Similarity NPC471026
0.6518 Remote Similarity NPC184915
0.6518 Remote Similarity NPC259294
0.6486 Remote Similarity NPC483170
0.6404 Remote Similarity NPC44782
0.6396 Remote Similarity NPC307400
0.6396 Remote Similarity NPC472204
0.6396 Remote Similarity NPC27289
0.6396 Remote Similarity NPC119583
0.6389 Remote Similarity NPC477331
0.6355 Remote Similarity NPC87153
0.633 Remote Similarity NPC477326
0.6283 Remote Similarity NPC115013
0.625 Remote Similarity NPC143421
0.6174 Remote Similarity NPC472200
0.6174 Remote Similarity NPC123204
0.6161 Remote Similarity NPC477319
0.614 Remote Similarity NPC290012
0.6091 Remote Similarity NPC89843
0.6036 Remote Similarity NPC477344
0.6036 Remote Similarity NPC600446
0.6036 Remote Similarity NPC605013
0.6018 Remote Similarity NPC472205
0.6 Remote Similarity NPC169345
0.6 Remote Similarity NPC604005
0.6 Remote Similarity NPC605014
0.5946 Remote Similarity NPC478734
0.5929 Remote Similarity NPC267592
0.5841 Remote Similarity NPC478733
0.5814 Remote Similarity NPC600940
0.5804 Remote Similarity NPC477332
0.578 Remote Similarity NPC477330
0.5776 Remote Similarity NPC478726
0.5766 Remote Similarity NPC113745
0.5766 Remote Similarity NPC477320
0.5766 Remote Similarity NPC477323
0.5766 Remote Similarity NPC477325
0.5766 Remote Similarity NPC609436
0.575 Remote Similarity NPC478727
0.5748 Remote Similarity NPC600672
0.5739 Remote Similarity NPC297768
0.5727 Remote Similarity NPC477329
0.5726 Remote Similarity NPC477317
0.5726 Remote Similarity NPC477318
0.5701 Remote Similarity NPC478729
0.5692 Remote Similarity NPC610997
0.5669 Remote Similarity NPC611287
0.5667 Remote Similarity NPC478728
0.5659 Remote Similarity NPC600721
0.5659 Remote Similarity NPC605872
0.5656 Remote Similarity NPC475241
0.5652 Remote Similarity NPC146992
0.5652 Remote Similarity NPC85759
0.5641 Remote Similarity NPC238264
0.5641 Remote Similarity NPC477345
0.5636 Remote Similarity NPC477328
0.5625 Remote Similarity NPC22742
0.5625 Remote Similarity NPC477346
0.5586 Remote Similarity NPC281563
0.5556 Remote Similarity NPC294748
0.5545 Remote Similarity NPC146380
0.5504 Remote Similarity NPC610996
0.5462 Remote Similarity NPC238056
0.5385 Remote Similarity NPC478722
0.5385 Remote Similarity NPC478725
0.5339 Remote Similarity NPC478723
0.5339 Remote Similarity NPC478724
0.5273 Remote Similarity NPC606819
0.5179 Remote Similarity NPC477350
0.5126 Remote Similarity NPC479061
0.5124 Remote Similarity NPC476087
0.5124 Remote Similarity NPC475667
0.5086 Remote Similarity NPC477349
0.5083 Remote Similarity NPC479060
0.5082 Remote Similarity NPC478732
0.5074 Remote Similarity NPC472352
0.5041 Remote Similarity NPC475270
0.5041 Remote Similarity NPC475327

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC147032 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