Natural Product: NPC146380

Natural Product IDNPC146380
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Pescaprein I
IUPAC Name n.a.
Synonyms Pescaprein I
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL507247
PubChem CID 21575466
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0000198] Oligosaccharides

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 NNQOYMNQPOXGDT-OIAOIZBASA-N
Standard InCHI InChI=1S/C58H102O23/c1-8-10-12-13-14-15-18-21-26-30-38(60)77-53-52(81-55-46(68)43(65)40(62)32(4)71-55)49(78-54-45(67)42(64)39(61)31(3)70-54)35(7)74-58(53)79-48-34(6)73-56-47(69)50(48)76-37(59)29-25-22-19-16-17-20-24-28-36(27-23-11-9-2)75-57-51(80-56)44(66)41(63)33(5)72-57/h31-36,39-58,61-69H,8-30H2,1-7H3/t31-,32-,33+,34-,35-,36-,39-,40-,41-,42+,43+,44-,45+,46+,47+,48-,49-,50-,51+,52+,53+,54-,55-,56-,57-,58-/m0/s1
SMILES CCCCCCCCCCCC(=O)O[C@H]1[C@@H](O[C@H]([C@@H]([C@H]1O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O)C)O[C@H]1[C@H](C)O[C@@H]2[C@@H]([C@@H]1OC(=O)CCCCCCCCC[C@@H](O[C@H]1[C@H](O2)[C@@H](O)[C@H]([C@H](O1)C)O)CCCCC)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1166.68 Volume:   1157.287
?
Van der Waals volume.
Dense:   1.008 LogP:   4.356
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.888
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.337
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The logarithm of aqueous solubility value.
Rotatable Bonds:   22.0 Rigid Bonds:   48.0
TPSA:   326.97
?
Topological Polar Surface Area.
H-Bond Acceptor:   23.0
H-Bond Donor:   9.0 Rings:   6.0
Heavy Atoms:   23.0

MedChem Properties

QED Drug-Likeness Score:   0.058 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.722 Fsp3:   0.966
MCE-18:   120.246
?
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:   0.992 Fluc inhibitor:   0.339
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
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:   0.535 Promiscuous compounds:   0.025

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.599 MDCK Permeability:   -4.967
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):   0.381
20% Bioavailability (F20%):   0.211 30% Bioavailability (F30%):   0.765
50% Bioavailability (F50%):   0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.987
Plasma Protein Binding (PPB):   93.467% Volume Distribution (VD):   -0.09
Fu: 5.163%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.947
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.019

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:   0.629
?
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):  0.717 Half-life (T1/2):  3.055

ADMET: Toxicity

hERG Blockers:  0.049 hERG Blockers (10um):  0.357
Human Hepatotoxicity (H-HT):  0.363 Drug-induced Liver Injury (DILI):  0.98
AMES Toxicity:  0.729 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.006 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.999
Hematotoxicity:  0.582 Drug-induced Nephrotoxicity:  0.924
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.725
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.506
BCF:   1.453
?
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:   4.857
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.0
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.197
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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
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[15730248]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota Leaves Khon Kaen, Thailand 2002-APR PMID[15921434]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[19061389]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota ground entire plants Hainan Province, China 2004-APR PMID[19061389]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. aerial part n.a. PMID[21338052]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[31017778]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23352 Ipomoea pes-caprae 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

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. ED50 = 5.0 ug ml-1 PMID[15730248]

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 NPC146380 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
0.9412 High Similarity NPC113745
0.9412 High Similarity NPC477320
0.9412 High Similarity NPC477323
0.9412 High Similarity NPC477325
0.9412 High Similarity NPC609436
0.9275 High Similarity NPC604005
0.9275 High Similarity NPC605014
0.8767 High Similarity NPC267592
0.8533 High Similarity NPC307400
0.8533 High Similarity NPC27289
0.8493 Intermediate Similarity NPC477326
0.84 Intermediate Similarity NPC477319
0.8289 Intermediate Similarity NPC143421
0.8289 Intermediate Similarity NPC472204
0.8101 Intermediate Similarity NPC123204
0.8077 Intermediate Similarity NPC290012
0.8056 Intermediate Similarity NPC281563
0.775 Intermediate Similarity NPC183888
0.775 Intermediate Similarity NPC259294
0.7639 Intermediate Similarity NPC477350
0.7532 Intermediate Similarity NPC600446
0.7532 Intermediate Similarity NPC605013
0.7531 Intermediate Similarity NPC126685
0.7361 Intermediate Similarity NPC606819
0.7356 Intermediate Similarity NPC124878
0.7356 Intermediate Similarity NPC231888
0.7273 Intermediate Similarity NPC35338
0.7273 Intermediate Similarity NPC204214
0.7273 Intermediate Similarity NPC92283
0.7079 Intermediate Similarity NPC63404
0.7073 Intermediate Similarity NPC483170
0.7 Intermediate Similarity NPC109887
0.6962 Remote Similarity NPC89843
0.6957 Remote Similarity NPC10121
0.6957 Remote Similarity NPC198918
0.6923 Remote Similarity NPC22742
0.6923 Remote Similarity NPC477349
0.6923 Remote Similarity NPC477346
0.6786 Remote Similarity NPC169345
0.6747 Remote Similarity NPC119583
0.6707 Remote Similarity NPC146992
0.6707 Remote Similarity NPC85759
0.6588 Remote Similarity NPC115013
0.6548 Remote Similarity NPC294748
0.6429 Remote Similarity NPC173328
0.6395 Remote Similarity NPC238056
0.6353 Remote Similarity NPC186992
0.6265 Remote Similarity NPC158302
0.6265 Remote Similarity NPC477344
0.625 Remote Similarity NPC10883
0.625 Remote Similarity NPC477329
0.6234 Remote Similarity NPC478729
0.6207 Remote Similarity NPC477317
0.6207 Remote Similarity NPC477318
0.6145 Remote Similarity NPC478734
0.6136 Remote Similarity NPC184915
0.6136 Remote Similarity NPC224953
0.6125 Remote Similarity NPC477330
0.6105 Remote Similarity NPC77651
0.6067 Remote Similarity NPC163409
0.6047 Remote Similarity NPC472205
0.6 Remote Similarity NPC478733
0.6 Remote Similarity NPC44782
0.5938 Remote Similarity NPC28069
0.5926 Remote Similarity NPC477328
0.5862 Remote Similarity NPC297768
0.5843 Remote Similarity NPC478731
0.5802 Remote Similarity NPC475425
0.5795 Remote Similarity NPC478730
0.573 Remote Similarity NPC238264
0.573 Remote Similarity NPC476087
0.573 Remote Similarity NPC475667
0.573 Remote Similarity NPC477345
0.5728 Remote Similarity NPC472352
0.5696 Remote Similarity NPC169085
0.5682 Remote Similarity NPC44682
0.5667 Remote Similarity NPC162925
0.5667 Remote Similarity NPC478732
0.5652 Remote Similarity NPC269318
0.5604 Remote Similarity NPC475270
0.5604 Remote Similarity NPC475327
0.5581 Remote Similarity NPC477331
0.5581 Remote Similarity NPC477332
0.5545 Remote Similarity NPC147032
0.5543 Remote Similarity NPC475525
0.5543 Remote Similarity NPC475540
0.549 Remote Similarity NPC471025
0.5484 Remote Similarity NPC476066
0.5446 Remote Similarity NPC290276
0.5426 Remote Similarity NPC475164
0.5426 Remote Similarity NPC478728
0.5393 Remote Similarity NPC479061
0.5376 Remote Similarity NPC472200
0.5368 Remote Similarity NPC478727
0.5368 Remote Similarity NPC473605
0.5368 Remote Similarity NPC475375
0.5341 Remote Similarity NPC479059
0.5333 Remote Similarity NPC478724
0.5333 Remote Similarity NPC479060
0.5278 Remote Similarity NPC206823
0.5258 Remote Similarity NPC475241
0.5222 Remote Similarity NPC478722
0.5222 Remote Similarity NPC478725
0.5189 Remote Similarity NPC600940
0.5185 Remote Similarity NPC471024
0.5169 Remote Similarity NPC216883
0.5165 Remote Similarity NPC479058
0.5165 Remote Similarity NPC478723
0.514 Remote Similarity NPC471026
0.5055 Remote Similarity NPC60849
0.5054 Remote Similarity NPC478726

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC146380 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