Natural Product: NPC478725

Natural Product IDNPC478725
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
ZDSCMHPEWOPANQ-TXECYITHSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44583808
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 ZDSCMHPEWOPANQ-TXECYITHSA-N
Standard InCHI InChI=1S/C67H116O28/c1-9-12-14-15-16-17-20-23-27-32-45(72)89-58-53(80)55(93-67-61(95-63-51(78)49(76)47(74)42(34-68)86-63)60(91-62(81)36(4)37(5)70)56(40(8)84-67)88-44(71)29-11-3)39(7)82-64(58)92-54-38(6)83-65-59(52(54)79)90-46(73)33-28-24-21-18-19-22-26-31-41(30-25-13-10-2)85-66-57(94-65)50(77)48(75)43(35-69)87-66/h36-43,47-61,63-70,74-80H,9-35H2,1-8H3/t36?,37?,38-,39-,40-,41?,42+,43+,47+,48+,49-,50-,51+,52+,53+,54-,55-,56-,57+,58+,59+,60+,61+,63+,64-,65+,66+,67-/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]2[C@@H]([C@@H]1O)OC(=O)CCCCCCCCCC(CCCCC)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O2)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)OC(=O)CCC)OC(=O)C(C)C(C)O)O[C@@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1368.77 Volume:   1351.629
?
Van der Waals volume.
Dense:   1.013 LogP:   4.341
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.502
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.08
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The logarithm of aqueous solubility value.
Rotatable Bonds:   32.0 Rigid Bonds:   50.0
TPSA:   399.8
?
Topological Polar Surface Area.
H-Bond Acceptor:   28.0
H-Bond Donor:   10.0 Rings:   6.0
Heavy Atoms:   28.0

MedChem Properties

QED Drug-Likeness Score:   0.029 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.686 Fsp3:   0.94
MCE-18:   126.923
?
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:   0.998 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.003
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.485 Promiscuous compounds:   0.132

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.554 MDCK Permeability:   -5.01
Pgp-inhibitor:   0.0 Pgp-substrate:   0.915
PAMPA:   0.996
?
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):   0.074
20% Bioavailability (F20%):   0.0 30% Bioavailability (F30%):   0.955
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.982
Plasma Protein Binding (PPB):   93.699% Volume Distribution (VD):   -0.194
Fu: 5.186%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.933

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:   0.001
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.997
?
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):  0.445 Half-life (T1/2):  3.572

ADMET: Toxicity

hERG Blockers:  0.015 hERG Blockers (10um):  0.048
Human Hepatotoxicity (H-HT):  0.432 Drug-induced Liver Injury (DILI):  0.964
AMES Toxicity:  0.101 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:  0.282 Drug-induced Nephrotoxicity:  0.949
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.406
A549 Cytotoxicity:  0.985 Hek293 Cytotoxicity:  0.125
BCF:   0.29
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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:   4.322
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.338
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.658
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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
NPO496 Ipomoea arborescens Species Convolvulaceae Eukaryota Roots n.a. n.a. PMID[16792407]
NPO496 Ipomoea arborescens 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
NPT148 Cell line HCT-15 Homo sapiens ED50 > 5.0 ug ml-1 PMID[16792407]
NPT382 Cell line OVCAR-5 Homo sapiens ED50 > 5.0 ug ml-1 PMID[16792407]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. ED50 > 5.0 ug ml-1 PMID[16792407]

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 NPC478725 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
0.96 High Similarity NPC478723
0.96 High Similarity NPC478724
0.9351 High Similarity NPC478726
0.8554 High Similarity NPC478728
0.8452 Intermediate Similarity NPC478727
0.825 Intermediate Similarity NPC478722
0.7654 Intermediate Similarity NPC477332
0.7179 Intermediate Similarity NPC478729
0.7059 Intermediate Similarity NPC109887
0.7037 Intermediate Similarity NPC477330
0.6966 Remote Similarity NPC184915
0.6966 Remote Similarity NPC224953
0.6829 Remote Similarity NPC477328
0.6824 Remote Similarity NPC477331
0.6813 Remote Similarity NPC44782
0.6747 Remote Similarity NPC477329
0.6667 Remote Similarity NPC238056
0.6628 Remote Similarity NPC89843
0.6517 Remote Similarity NPC297768
0.6395 Remote Similarity NPC22742
0.6395 Remote Similarity NPC477346
0.6386 Remote Similarity NPC477350
0.6344 Remote Similarity NPC472200
0.6264 Remote Similarity NPC119583
0.6222 Remote Similarity NPC146992
0.6222 Remote Similarity NPC85759
0.6207 Remote Similarity NPC477349
0.619 Remote Similarity NPC600940
0.618 Remote Similarity NPC477344
0.617 Remote Similarity NPC163409
0.6129 Remote Similarity NPC169345
0.6129 Remote Similarity NPC115013
0.6087 Remote Similarity NPC294748
0.6067 Remote Similarity NPC478734
0.6022 Remote Similarity NPC483170
0.6019 Remote Similarity NPC290276
0.6 Remote Similarity NPC600446
0.6 Remote Similarity NPC605013
0.5934 Remote Similarity NPC478733
0.5882 Remote Similarity NPC28069
0.5882 Remote Similarity NPC77651
0.5872 Remote Similarity NPC471024
0.5851 Remote Similarity NPC238264
0.5851 Remote Similarity NPC477345
0.5824 Remote Similarity NPC477326
0.5778 Remote Similarity NPC604005
0.5778 Remote Similarity NPC605014
0.5773 Remote Similarity NPC269318
0.5755 Remote Similarity NPC471025
0.5745 Remote Similarity NPC472204
0.5745 Remote Similarity NPC186992
0.5729 Remote Similarity NPC183888
0.5729 Remote Similarity NPC259294
0.5729 Remote Similarity NPC126685
0.57 Remote Similarity NPC475241
0.566 Remote Similarity NPC610996
0.5652 Remote Similarity NPC479059
0.5638 Remote Similarity NPC173328
0.5625 Remote Similarity NPC477317
0.5625 Remote Similarity NPC477318
0.5579 Remote Similarity NPC478730
0.5556 Remote Similarity NPC600721
0.5556 Remote Similarity NPC605872
0.5545 Remote Similarity NPC471026
0.5532 Remote Similarity NPC479061
0.5532 Remote Similarity NPC60849
0.5484 Remote Similarity NPC216883
0.5474 Remote Similarity NPC479060
0.5464 Remote Similarity NPC478732
0.5464 Remote Similarity NPC478731
0.5455 Remote Similarity NPC477347
0.5455 Remote Similarity NPC610997
0.5444 Remote Similarity NPC281563
0.5421 Remote Similarity NPC10883
0.5408 Remote Similarity NPC479057
0.5408 Remote Similarity NPC475270
0.5408 Remote Similarity NPC475327
0.5402 Remote Similarity NPC606819
0.5385 Remote Similarity NPC147032
0.5361 Remote Similarity NPC476087
0.5361 Remote Similarity NPC475667
0.5319 Remote Similarity NPC158302
0.5312 Remote Similarity NPC472205
0.5312 Remote Similarity NPC476781
0.53 Remote Similarity NPC476066
0.5256 Remote Similarity NPC206823
0.5222 Remote Similarity NPC475425
0.5222 Remote Similarity NPC146380
0.5208 Remote Similarity NPC267592
0.52 Remote Similarity NPC475525
0.52 Remote Similarity NPC475540
0.5196 Remote Similarity NPC473605
0.5196 Remote Similarity NPC475375
0.5161 Remote Similarity NPC113745
0.5161 Remote Similarity NPC477320
0.5161 Remote Similarity NPC477323
0.5161 Remote Similarity NPC477325
0.5161 Remote Similarity NPC609436
0.5155 Remote Similarity NPC477319
0.5138 Remote Similarity NPC611287
0.5102 Remote Similarity NPC143421
0.5102 Remote Similarity NPC307400
0.5102 Remote Similarity NPC27289
0.5098 Remote Similarity NPC475164

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC478725 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