Natural Product: NPC485319

Natural Product IDNPC485319
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
AQAYAGFMEBWASB-GHRWRXLVSA-M
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44575396
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 AQAYAGFMEBWASB-GHRWRXLVSA-M
Standard InCHI InChI=1S/C55H84O26S.Na/c1-24(2)12-11-17-53(9)55(66)34(74-26(4)57)20-52(8)28-13-14-32-50(5,6)33(16-18-51(32,7)27(28)15-19-54(52,55)49(65)80-53)76-48-44(36(60)31(23-72-48)81-82(67,68)69)79-46-38(62)37(61)41(25(3)73-46)77-45-39(63)42(29(58)22-71-45)78-47-40(64)43(70-10)35(59)30(21-56)75-47;/h11-13,17,25,27,29-48,56,58-64,66H,14-16,18-23H2,1-10H3,(H,67,68,69);/q;+1/p-1/b17-11-;/t25-,27-,29-,30-,31-,32+,33+,34+,35-,36+,37-,38-,39-,40-,41-,42+,43+,44-,45+,46+,47+,48+,51-,52+,53+,54-,55+;/m1./s1
SMILES CC(=C/C=C[C@@]1(C)[C@]2([C@H](C[C@@]3(C)C4=CC[C@H]5C(C)(C)[C@H](CC[C@]5(C)[C@@H]4CC[C@]23C(=O)O1)O[C@H]1[C@@H]([C@H]([C@@H](CO1)OS(=O)(=O)[O-])O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C)O1)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)OC)O)O)O)O)OC(=O)C)O)C.[Na+]

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1191.49 Volume:   1115.382
?
Van der Waals volume.
Dense:   1.068 LogP:   0.974
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.832
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.337
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The logarithm of aqueous solubility value.
Rotatable Bonds:   16.0 Rigid Bonds:   54.0
TPSA:   384.17
?
Topological Polar Surface Area.
H-Bond Acceptor:   26.0
H-Bond Donor:   9.0 Rings:   9.0
Heavy Atoms:   27.0

MedChem Properties

QED Drug-Likeness Score:   0.032 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.832 Fsp3:   0.855
MCE-18:   274.235
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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:   0.996 Fluc inhibitor:   0.064
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.022
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.346 Promiscuous compounds:   0.243

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.043 MDCK Permeability:   -5.359
Pgp-inhibitor:   0.017 Pgp-substrate:   0.001
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):   0.241
20% Bioavailability (F20%):   0.001 30% Bioavailability (F30%):   0.941
50% Bioavailability (F50%):   0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.286
Plasma Protein Binding (PPB):   70.224% Volume Distribution (VD):   -0.669
Fu: 26.917%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
BSEP inhibitor:   0.565

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.22 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.009 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.037
HLM stability:   0.478
?
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):  0.147 Half-life (T1/2):  3.292

ADMET: Toxicity

hERG Blockers:  0.002 hERG Blockers (10um):  0.005
Human Hepatotoxicity (H-HT):  0.912 Drug-induced Liver Injury (DILI):  0.996
AMES Toxicity:  0.965 Rat Oral Acute Toxicity:  0.02
Maximum Recommended Daily Dose:  0.036 Skin Sensitization:  1.0
Carcinogencity:  0.022 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.999
Hematotoxicity:  0.678 Drug-induced Nephrotoxicity:  0.892
Genotoxicity:  0.999 RPMI-8226 Immunitoxicity:  0.194
A549 Cytotoxicity:  0.11 Hek293 Cytotoxicity:  0.117
BCF:   0.446
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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:   3.207
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.837
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.739
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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
NPO40689 Mensamaria intercedens lampert n.a. n.a. n.a. n.a. n.a. n.a. PMID[12932123]
NPO40689 Mensamaria intercedens lampert n.a. n.a. n.a. n.a. n.a. n.a. PMID[15844944]

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
NPT81 Cell line A549 Homo sapiens ED50 = 1.4 ug ml-1 PMID[15844944]
NPT83 Cell line MCF7 Homo sapiens ED50 = 1.8 ug ml-1 PMID[15844944]
NPT309 Cell line 1A9 Homo sapiens ED50 = 0.96 ug ml-1 PMID[15844944]
NPT308 Cell line CAKI-1 Homo sapiens ED50 = 1.0 ug ml-1 PMID[15844944]
NPT306 Cell line PC-3 Homo sapiens ED50 = 2.2 ug ml-1 PMID[15844944]
NPT91 Cell line KB Homo sapiens ED50 = 3.0 ug ml-1 PMID[15844944]
NPT147 Cell line SK-MEL-2 Homo sapiens ED50 = 2.2 ug ml-1 PMID[15844944]
NPT180 Cell line HCT-8 Homo sapiens ED50 = 1.9 ug ml-1 PMID[15844944]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. ED50 = 3.2 ug ml-1 PMID[15844944]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. ED50 = 3.7 ug ml-1 PMID[15844944]

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 NPC485319 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
0.9333 High Similarity NPC485315
0.8852 High Similarity NPC485316
0.8062 Intermediate Similarity NPC485317
0.7939 Intermediate Similarity NPC485275
0.7313 Intermediate Similarity NPC610857
0.6912 Remote Similarity NPC485318
0.6667 Remote Similarity NPC485273
0.6224 Remote Similarity NPC482870
0.619 Remote Similarity NPC481606
0.6127 Remote Similarity NPC485686
0.6014 Remote Similarity NPC485687
0.5629 Remote Similarity NPC485274
0.5563 Remote Similarity NPC481603
0.5532 Remote Similarity NPC484546
0.5455 Remote Similarity NPC484545
0.5448 Remote Similarity NPC606029
0.5385 Remote Similarity NPC477233
0.5385 Remote Similarity NPC477236
0.5342 Remote Similarity NPC477232
0.5316 Remote Similarity NPC481604
0.5315 Remote Similarity NPC477235
0.5256 Remote Similarity NPC478069
0.5241 Remote Similarity NPC477234
0.5033 Remote Similarity NPC482867

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC485319 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