Natural Product: NPC471025

Natural Product IDNPC471025
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Purgin Iii
IUPAC Name n.a.
Synonyms Purgin III
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2336637
PubChem CID 71720092
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 RIGNHXXJJDXLEF-COBCPTSWSA-N
Standard InCHI InChI=1S/C142H228O54/c1-13-19-25-27-31-39-57-71-99(151)187-131-129(195-134-111(163)106(158)103(155)91(77-143)177-134)121(191-136-115(167)124(184-101(153)75-73-87-59-49-43-50-60-87)119(83(9)170-136)181-95(147)67-47-23-17-5)85(11)173-141(131)189-117-81(7)169-133(112(164)109(117)161)193-126-107(159)104(156)92(78-144)178-139(126)175-89(63-45-21-15-3)65-53-37-33-29-35-41-55-69-97(149)183-123-94(80-146)180-135(113(165)110(123)162)196-130-122(192-137-116(168)125(185-102(154)76-74-88-61-51-44-52-62-88)120(84(10)171-137)182-96(148)68-48-24-18-6)86(12)174-142(132(130)188-100(152)72-58-40-32-28-26-20-14-2)190-118-82(8)172-138-128(114(118)166)186-98(150)70-56-42-36-30-34-38-54-66-90(64-46-22-16-4)176-140-127(194-138)108(160)105(157)93(79-145)179-140/h43-44,49-52,59-62,73-76,81-86,89-94,103-146,155-168H,13-42,45-48,53-58,63-72,77-80H2,1-12H3/b75-73+,76-74+/t81-,82-,83-,84-,85-,86-,89-,90-,91+,92+,93+,94+,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+,133-,134-,135-,136-,137-,138-,139+,140+,141-,142-/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)CCCCC)O)O)CCCCC)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)OC(=O)/C=C/c1ccccc1)OC(=O)CCCCC)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:   2797.51 Volume:   2785.841
?
Van der Waals volume.
Dense:   1.004 LogP:   11.015
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   7.92
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -7.344
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   80.0 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:   9.324 Fsp3:   0.831
MCE-18:   349.615
?
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:   0.031
?
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:   0.241

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.841 MDCK Permeability:   -5.412
Pgp-inhibitor:   0.0 Pgp-substrate:   0.999
PAMPA:   0.993
?
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):   0.982
20% Bioavailability (F20%):   0.755 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.73
Plasma Protein Binding (PPB):   96.41% Volume Distribution (VD):   -0.29
Fu: 2.55%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.821

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:   0.033
?
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):  -0.506 Half-life (T1/2):  8.741

ADMET: Toxicity

hERG Blockers:  0.062 hERG Blockers (10um):  0.023
Human Hepatotoxicity (H-HT):  0.672 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  0.769 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:  0.603 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.909
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.911
BCF:   -0.354
?
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:   6.71
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   8.667
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   6.021
?
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 = 6.5 n.a. PMID[10328288]
NPT668 Individual protein P-glycoprotein 1 Homo sapiens FC = 6.4 n.a. PMID[10328288]

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[24913558]
NPT83 Cell line MCF7 Homo sapiens FC = 4.7 n.a. PMID[10328288]

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 NPC471025 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 NPC471024
0.8673 High Similarity NPC77651
0.8611 High Similarity NPC147032
0.7767 Intermediate Similarity NPC28069
0.7547 Intermediate Similarity NPC10883
0.7383 Intermediate Similarity NPC290276
0.6916 Remote Similarity NPC124878
0.6916 Remote Similarity NPC231888
0.6909 Remote Similarity NPC10121
0.6909 Remote Similarity NPC198918
0.6852 Remote Similarity NPC35338
0.6852 Remote Similarity NPC204214
0.6852 Remote Similarity NPC92283
0.6768 Remote Similarity NPC109887
0.6697 Remote Similarity NPC63404
0.6602 Remote Similarity NPC162925
0.6552 Remote Similarity NPC471026
0.6337 Remote Similarity NPC477326
0.6226 Remote Similarity NPC184915
0.6226 Remote Similarity NPC224953
0.62 Remote Similarity NPC87153
0.6176 Remote Similarity NPC600446
0.6176 Remote Similarity NPC605013
0.6111 Remote Similarity NPC44782
0.6075 Remote Similarity NPC183888
0.6075 Remote Similarity NPC259294
0.598 Remote Similarity NPC604005
0.598 Remote Similarity NPC605014
0.5926 Remote Similarity NPC126685
0.5816 Remote Similarity NPC478729
0.5755 Remote Similarity NPC478725
0.5743 Remote Similarity NPC477330
0.5741 Remote Similarity NPC478726
0.5728 Remote Similarity NPC113745
0.5728 Remote Similarity NPC477320
0.5728 Remote Similarity NPC477323
0.5728 Remote Similarity NPC477325
0.5728 Remote Similarity NPC609436
0.5727 Remote Similarity NPC472200
0.5701 Remote Similarity NPC478723
0.5701 Remote Similarity NPC478724
0.5686 Remote Similarity NPC281563
0.5686 Remote Similarity NPC477329
0.5648 Remote Similarity NPC472204
0.5648 Remote Similarity NPC119583
0.5596 Remote Similarity NPC483170
0.5588 Remote Similarity NPC477328
0.5545 Remote Similarity NPC115013
0.5505 Remote Similarity NPC307400
0.5505 Remote Similarity NPC27289
0.549 Remote Similarity NPC146380
0.5472 Remote Similarity NPC89843
0.5472 Remote Similarity NPC477331
0.5463 Remote Similarity NPC478722
0.5463 Remote Similarity NPC267592
0.5439 Remote Similarity NPC478727
0.5421 Remote Similarity NPC477344
0.5413 Remote Similarity NPC477319
0.5405 Remote Similarity NPC169345
0.5392 Remote Similarity NPC477350
0.5364 Remote Similarity NPC143421
0.5351 Remote Similarity NPC478728
0.5347 Remote Similarity NPC606819
0.5327 Remote Similarity NPC478734
0.5327 Remote Similarity NPC477332
0.531 Remote Similarity NPC123204
0.5273 Remote Similarity NPC472205
0.5268 Remote Similarity NPC290012
0.5268 Remote Similarity NPC477317
0.5268 Remote Similarity NPC477318
0.5229 Remote Similarity NPC478733
0.5179 Remote Similarity NPC238264
0.5179 Remote Similarity NPC477345
0.514 Remote Similarity NPC22742
0.514 Remote Similarity NPC477349
0.514 Remote Similarity NPC477346
0.5135 Remote Similarity NPC297768
0.5045 Remote Similarity NPC479061
0.5039 Remote Similarity NPC600940

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471025 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