Natural Product: NPC92283

Natural Product IDNPC92283
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Pescaprein Xxi
IUPAC Name n.a.
Synonyms Pescaprein XXI
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1773737
PubChem CID 52952205
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 NDKPFZJXDUTDOW-YEMYNBOPSA-N
Standard InCHI InChI=1S/C72H116O25/c1-10-13-15-16-17-18-21-24-32-38-50(74)92-66-65(97-68-56(80)54(78)52(76)42(5)84-68)61(94-69-57(81)62(59(44(7)86-69)93-67(83)41(4)12-3)91-51(75)40-39-47-33-28-26-29-34-47)46(9)88-72(66)95-60-45(8)87-70-58(82)63(60)90-49(73)37-31-25-22-19-20-23-30-36-48(35-27-14-11-2)89-71-64(96-70)55(79)53(77)43(6)85-71/h26,28-29,33-34,39-46,48,52-66,68-72,76-82H,10-25,27,30-32,35-38H2,1-9H3/b40-39+/t41-,42-,43+,44-,45-,46-,48-,52-,53-,54+,55-,56+,57+,58+,59-,60-,61-,62-,63-,64+,65+,66+,68-,69-,70-,71-,72-/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)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]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:   1380.78 Volume:   1392.636
?
Van der Waals volume.
Dense:   0.991 LogP:   6.915
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   5.259
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -5.648
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   30.0 Rigid Bonds:   57.0
TPSA:   339.11
?
Topological Polar Surface Area.
H-Bond Acceptor:   25.0
H-Bond Donor:   7.0 Rings:   7.0
Heavy Atoms:   25.0

MedChem Properties

QED Drug-Likeness Score:   0.019 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.968 Fsp3:   0.833
MCE-18:   187.106
?
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:   0.666
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.219
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.319
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.382 Promiscuous compounds:   0.016

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.511 MDCK Permeability:   -5.018
Pgp-inhibitor:   0.007 Pgp-substrate:   0.97
PAMPA:   0.985
?
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):   0.025
20% Bioavailability (F20%):   0.331 30% Bioavailability (F30%):   0.97
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.992
Plasma Protein Binding (PPB):   96.863% Volume Distribution (VD):   -0.056
Fu: 2.366%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.956
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.969

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.004
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.147
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.888
?
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):  0.762 Half-life (T1/2):  3.876

ADMET: Toxicity

hERG Blockers:  0.114 hERG Blockers (10um):  0.382
Human Hepatotoxicity (H-HT):  0.535 Drug-induced Liver Injury (DILI):  0.995
AMES Toxicity:  0.608 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.003 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.002 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.997
Hematotoxicity:  0.664 Drug-induced Nephrotoxicity:  0.983
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.786
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.796
BCF:   0.681
?
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:   5.102
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.597
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.486
?
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
NPT389 Cell line RPMI-8226 Homo sapiens IC50 > 10000.0 nM PMID[34969245]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[34969245]
NPT25439 Cell line MM1.S Homo sapiens Activity n.a. n.a. n.a. PMID[34969245]
NPT2 Others Unspecified n.a. Ratio IC50 = 3.3 n.a. PMID[21338052]

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 NPC92283 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
1.0 High Similarity NPC35338
1.0 High Similarity NPC204214
0.9775 High Similarity NPC63404
0.9444 High Similarity NPC124878
0.9444 High Similarity NPC231888
0.8947 High Similarity NPC10121
0.8947 High Similarity NPC198918
0.875 High Similarity NPC10883
0.7727 Intermediate Similarity NPC147032
0.7527 Intermediate Similarity NPC307400
0.7527 Intermediate Similarity NPC27289
0.7525 Intermediate Similarity NPC77651
0.7419 Intermediate Similarity NPC477319
0.7407 Intermediate Similarity NPC471024
0.734 Intermediate Similarity NPC143421
0.734 Intermediate Similarity NPC472204
0.7308 Intermediate Similarity NPC290276
0.7273 Intermediate Similarity NPC146380
0.7216 Intermediate Similarity NPC123204
0.7188 Intermediate Similarity NPC290012
0.7019 Intermediate Similarity NPC28069
0.6957 Remote Similarity NPC113745
0.6957 Remote Similarity NPC477320
0.6957 Remote Similarity NPC477323
0.6957 Remote Similarity NPC477325
0.6957 Remote Similarity NPC609436
0.6947 Remote Similarity NPC267592
0.6939 Remote Similarity NPC183888
0.6939 Remote Similarity NPC259294
0.6882 Remote Similarity NPC604005
0.6882 Remote Similarity NPC605014
0.6852 Remote Similarity NPC471025
0.6837 Remote Similarity NPC162925
0.6768 Remote Similarity NPC126685
0.64 Remote Similarity NPC483170
0.6392 Remote Similarity NPC477326
0.6289 Remote Similarity NPC89843
0.6263 Remote Similarity NPC146992
0.6263 Remote Similarity NPC85759
0.625 Remote Similarity NPC22742
0.625 Remote Similarity NPC477346
0.6211 Remote Similarity NPC281563
0.6176 Remote Similarity NPC169345
0.6139 Remote Similarity NPC294748
0.6139 Remote Similarity NPC119583
0.6019 Remote Similarity NPC238056
0.6019 Remote Similarity NPC115013
0.5918 Remote Similarity NPC87153
0.59 Remote Similarity NPC158302
0.59 Remote Similarity NPC600446
0.59 Remote Similarity NPC605013
0.5882 Remote Similarity NPC173328
0.5763 Remote Similarity NPC471026
0.5743 Remote Similarity NPC477344
0.5729 Remote Similarity NPC477350
0.5728 Remote Similarity NPC472205
0.5714 Remote Similarity NPC477317
0.5714 Remote Similarity NPC477318
0.5673 Remote Similarity NPC186992
0.566 Remote Similarity NPC184915
0.566 Remote Similarity NPC224953
0.5644 Remote Similarity NPC478734
0.5556 Remote Similarity NPC44782
0.5534 Remote Similarity NPC478733
0.5521 Remote Similarity NPC606819
0.5472 Remote Similarity NPC238264
0.5472 Remote Similarity NPC477345
0.5446 Remote Similarity NPC477349
0.5429 Remote Similarity NPC297768
0.5385 Remote Similarity NPC109887
0.5372 Remote Similarity NPC472352
0.5327 Remote Similarity NPC476087
0.5327 Remote Similarity NPC475667
0.5278 Remote Similarity NPC478732
0.5273 Remote Similarity NPC269318
0.5229 Remote Similarity NPC475270
0.5229 Remote Similarity NPC475327
0.5225 Remote Similarity NPC475164
0.5192 Remote Similarity NPC477331
0.5088 Remote Similarity NPC140561
0.5088 Remote Similarity NPC475241
0.5045 Remote Similarity NPC163409
0.5045 Remote Similarity NPC472200
0.5044 Remote Similarity NPC473605
0.5044 Remote Similarity NPC475375
0.5041 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 NPC92283 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