Natural Product: NPC484833

Natural Product IDNPC484833
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
DOQIKJQGQOOLJK-UOGFOJPVSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44584126
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene saponins

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 DOQIKJQGQOOLJK-UOGFOJPVSA-N
Standard InCHI InChI=1S/C62H96O27/c1-12-26(4)52(79)89-49-50(84-35(67)19-25(2)3)62(24-65)28(20-57(49,5)6)27-13-14-33-59(9)17-16-34(58(7,8)32(59)15-18-60(33,10)61(27,11)47(75)48(62)76)83-56-46(88-55-42(74)39(71)37(69)30(21-63)81-55)44(85-53-40(72)36(68)29(66)23-80-53)43(45(87-56)51(77)78)86-54-41(73)38(70)31(22-64)82-54/h12-13,19,28-34,36-50,53-56,63-66,68-76H,14-18,20-24H2,1-11H3,(H,77,78)/b26-12-/t28-,29-,30-,31-,32+,33-,34+,36-,37-,38-,39+,40+,41+,42-,43+,44+,45+,46-,47+,48-,49+,50+,53-,54-,55+,56-,59+,60-,61+,62+/m1/s1
SMILES C/C=C(/C)C(=O)O[C@H]1[C@@H]([C@@]2(CO)[C@H](CC1(C)C)C1=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)[C@H]([C@H]2O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O1)O[C@@H]1[C@H]([C@@H]([C@@H](CO)O1)O)O)O[C@@H]1[C@H]([C@@H]([C@@H](CO1)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC(=O)C=C(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1272.61 Volume:   1225.417
?
Van der Waals volume.
Dense:   1.039 LogP:   0.844
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.874
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.307
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The logarithm of aqueous solubility value.
Rotatable Bonds:   18.0 Rigid Bonds:   54.0
TPSA:   426.73
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Topological Polar Surface Area.
H-Bond Acceptor:   27.0
H-Bond Donor:   14.0 Rings:   9.0
Heavy Atoms:   27.0

MedChem Properties

QED Drug-Likeness Score:   0.037 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.477 Fsp3:   0.855
MCE-18:   206.226
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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:   0.832 Fluc inhibitor:   0.008
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.233 Promiscuous compounds:   0.311

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.298 MDCK Permeability:   -5.186
Pgp-inhibitor:   0.0 Pgp-substrate:   0.98
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):   0.976
20% Bioavailability (F20%):   0.885 30% Bioavailability (F30%):   0.998
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.359
Plasma Protein Binding (PPB):   69.465% Volume Distribution (VD):   -0.396
Fu: 17.561%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

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:   0.644 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.57
HLM stability:   0.0
?
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):  -0.703 Half-life (T1/2):  4.257

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.44 Drug-induced Liver Injury (DILI):  0.909
AMES Toxicity:  0.525 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.002 Skin Sensitization:  1.0
Carcinogencity:  0.009 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.39 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  0.167 RPMI-8226 Immunitoxicity:  0.144
A549 Cytotoxicity:  0.072 Hek293 Cytotoxicity:  0.039
BCF:   0.287
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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:   3.425
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.587
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.273
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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
NPO17377 Pittosporum viridiflorum Species Pittosporaceae Eukaryota n.a. n.a. n.a. PMID[11809069]
NPO17377 Pittosporum viridiflorum Species Pittosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17377 Pittosporum viridiflorum Species Pittosporaceae 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
NPT179 Cell line A2780 Homo sapiens IC50 = 10.1 ug.mL-1 PMID[11809069]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IC12 = 85.0 ug ml-1 PMID[11809069]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IC12 = 80.0 ug ml-1 PMID[11809069]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IC12 = 140.0 ug ml-1 PMID[11809069]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IC12 = 100.0 ug ml-1 PMID[11809069]

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 NPC484833 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
0.7815 Intermediate Similarity NPC192765
0.7807 Intermediate Similarity NPC329976
0.7769 Intermediate Similarity NPC262796
0.7769 Intermediate Similarity NPC45346
0.775 Intermediate Similarity NPC178264
0.7642 Intermediate Similarity NPC475377
0.7642 Intermediate Similarity NPC476074
0.7073 Intermediate Similarity NPC264566
0.7045 Intermediate Similarity NPC150893
0.7016 Intermediate Similarity NPC46823
0.6935 Remote Similarity NPC602995
0.6825 Remote Similarity NPC71391
0.6807 Remote Similarity NPC470914
0.6794 Remote Similarity NPC329960
0.6694 Remote Similarity NPC477077
0.6694 Remote Similarity NPC477078
0.6667 Remote Similarity NPC271610
0.6667 Remote Similarity NPC25998
0.6585 Remote Similarity NPC605294
0.6562 Remote Similarity NPC329923
0.6562 Remote Similarity NPC475281
0.6532 Remote Similarity NPC478152
0.6532 Remote Similarity NPC478151
0.6364 Remote Similarity NPC470913
0.6328 Remote Similarity NPC478150
0.632 Remote Similarity NPC477197
0.632 Remote Similarity NPC606553
0.6308 Remote Similarity NPC329828
0.6231 Remote Similarity NPC473918
0.6212 Remote Similarity NPC488308
0.6212 Remote Similarity NPC476780
0.6183 Remote Similarity NPC475167
0.6165 Remote Similarity NPC312650
0.6107 Remote Similarity NPC277212
0.6107 Remote Similarity NPC30279
0.6074 Remote Similarity NPC476777
0.597 Remote Similarity NPC265841
0.5956 Remote Similarity NPC329657
0.5942 Remote Similarity NPC488309
0.5923 Remote Similarity NPC478600
0.5923 Remote Similarity NPC478599
0.5906 Remote Similarity NPC477193
0.5868 Remote Similarity NPC603026
0.5846 Remote Similarity NPC609119
0.5827 Remote Similarity NPC477075
0.5827 Remote Similarity NPC477076
0.5809 Remote Similarity NPC329993
0.5778 Remote Similarity NPC134914
0.5778 Remote Similarity NPC473755
0.5714 Remote Similarity NPC295408
0.5683 Remote Similarity NPC173435
0.5683 Remote Similarity NPC172374
0.5683 Remote Similarity NPC478064
0.5662 Remote Similarity NPC478598
0.5649 Remote Similarity NPC107536
0.5649 Remote Similarity NPC280029
0.5649 Remote Similarity NPC9470
0.5615 Remote Similarity NPC477194
0.5612 Remote Similarity NPC110700
0.5564 Remote Similarity NPC478155
0.5564 Remote Similarity NPC478154
0.5547 Remote Similarity NPC470518
0.5515 Remote Similarity NPC470912
0.5507 Remote Similarity NPC476774
0.5496 Remote Similarity NPC609281
0.5468 Remote Similarity NPC225791
0.5462 Remote Similarity NPC477191
0.5429 Remote Similarity NPC476779
0.5379 Remote Similarity NPC187290
0.5357 Remote Similarity NPC475513
0.5338 Remote Similarity NPC477195
0.5324 Remote Similarity NPC484061
0.5324 Remote Similarity NPC484062
0.5319 Remote Similarity NPC484059
0.5319 Remote Similarity NPC484060
0.5315 Remote Similarity NPC476775
0.5299 Remote Similarity NPC477196
0.529 Remote Similarity NPC47995
0.5252 Remote Similarity NPC301639
0.5252 Remote Similarity NPC478065
0.5217 Remote Similarity NPC283417
0.5217 Remote Similarity NPC200049
0.5188 Remote Similarity NPC477192
0.517 Remote Similarity NPC69425
0.5143 Remote Similarity NPC82380
0.5143 Remote Similarity NPC244296
0.5137 Remote Similarity NPC476778
0.5116 Remote Similarity NPC605226
0.5113 Remote Similarity NPC477079
0.5105 Remote Similarity NPC478153
0.5102 Remote Similarity NPC476776
0.5074 Remote Similarity NPC470475
0.5036 Remote Similarity NPC609305

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC484833 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