Natural Product: NPC170953

Natural Product IDNPC170953
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GKQGIQVSMCHAFX-IBEHDNSVSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 88687
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides

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 GKQGIQVSMCHAFX-IBEHDNSVSA-N
Standard InCHI InChI=1S/C16H24O6/c1-8(2)10-5-4-9(3)6-11(10)21-16-15(20)14(19)13(18)12(7-17)22-16/h4-6,8,12-20H,7H2,1-3H3/t12-,13-,14+,15-,16-/m1/s1
SMILES CC(C)c1ccc(C)cc1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   312.16 Volume:   313.011
?
Van der Waals volume.
Dense:   0.997 LogP:   1.656
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.036
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.274
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   12.0
TPSA:   99.38
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.638 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.471 Fsp3:   0.625
MCE-18:   50.769
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.588 Fluc inhibitor:   0.006
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.027
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.049
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.242 Promiscuous compounds:   0.02

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.219 MDCK Permeability:   -4.925
Pgp-inhibitor:   0.021 Pgp-substrate:   0.145
PAMPA:   0.333
?
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):   0.023
20% Bioavailability (F20%):   0.036 30% Bioavailability (F30%):   0.701
50% Bioavailability (F50%):   0.621

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.088 MRP1:   0.942
Plasma Protein Binding (PPB):   88.113% Volume Distribution (VD):   -0.113
Fu: 11.853%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.997 BCRP inhibitor:   0.003
BSEP inhibitor:   0.706

ADMET: Metabolism

CYP1A2-inhibitor:   0.083 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.049 CYP2C19-substrate:   0.009
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.006
CYP3A4-inhibitor:   0.164 CYP3A4-substrate:   0.02
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.93
HLM stability:   0.252
?
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):  3.013 Half-life (T1/2):  2.712

ADMET: Toxicity

hERG Blockers:  0.038 hERG Blockers (10um):  0.173
Human Hepatotoxicity (H-HT):  0.691 Drug-induced Liver Injury (DILI):  0.628
AMES Toxicity:  0.792 Rat Oral Acute Toxicity:  0.028
Maximum Recommended Daily Dose:  0.016 Skin Sensitization:  0.992
Carcinogencity:  0.335 Eye Corrosion:  0.003
Eye Irritation:  0.55 Respiratory Toxicity:  0.023
Drug-induced Neurotoxicity:  0.026 Ototoxicity:  0.936
Hematotoxicity:  0.495 Drug-induced Nephrotoxicity:  0.766
Genotoxicity:  0.052 RPMI-8226 Immunitoxicity:  0.068
A549 Cytotoxicity:  0.117 Hek293 Cytotoxicity:  0.103
BCF:   1.296
?
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:   3.161
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.112
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.755
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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
NPO1905 Fagraea fragrans Species Gentianaceae Eukaryota bark and leaves Koh Kong Province, Cambodia 2005-DEC PMID[19053508]
NPO3796 Pseudomonas viridiflava Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO53 Nephelium mutabile Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4713 Eucalyptus cordata Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2839 Dovyalis abyssinica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3212 Bipolaris sorokiniana Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5020 Jasonia montana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3796 Pseudomonas viridiflava Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO1905 Fagraea fragrans Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2839 Dovyalis abyssinica Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5020 Jasonia montana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3212 Bipolaris sorokiniana Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO53 Nephelium mutabile Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4713 Eucalyptus cordata Species Myrtaceae 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

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 NPC170953 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
0.6038 Remote Similarity NPC608788
0.5849 Remote Similarity NPC299144
0.5781 Remote Similarity NPC146837
0.5769 Remote Similarity NPC294470
0.5741 Remote Similarity NPC12308
0.5741 Remote Similarity NPC226712
0.5686 Remote Similarity NPC212729
0.5686 Remote Similarity NPC604498
0.5636 Remote Similarity NPC69513
0.5614 Remote Similarity NPC218685
0.5577 Remote Similarity NPC217854
0.5577 Remote Similarity NPC269242
0.5538 Remote Similarity NPC5029
0.5538 Remote Similarity NPC30432
0.5536 Remote Similarity NPC48863
0.5536 Remote Similarity NPC251981
0.5536 Remote Similarity NPC13745
0.551 Remote Similarity NPC228907
0.5484 Remote Similarity NPC134260
0.5455 Remote Similarity NPC200092
0.5439 Remote Similarity NPC215833
0.5397 Remote Similarity NPC610808
0.5385 Remote Similarity NPC276195
0.537 Remote Similarity NPC152722
0.5345 Remote Similarity NPC49074
0.5312 Remote Similarity NPC600107
0.5303 Remote Similarity NPC278329
0.5273 Remote Similarity NPC60589
0.5273 Remote Similarity NPC469708
0.5273 Remote Similarity NPC609376
0.5263 Remote Similarity NPC166040
0.5263 Remote Similarity NPC604209
0.5254 Remote Similarity NPC162093
0.5254 Remote Similarity NPC485268
0.5254 Remote Similarity NPC205054
0.5254 Remote Similarity NPC606892
0.5246 Remote Similarity NPC222455
0.5172 Remote Similarity NPC40377
0.5172 Remote Similarity NPC9912
0.5167 Remote Similarity NPC26653
0.5167 Remote Similarity NPC164599
0.5167 Remote Similarity NPC210478
0.5156 Remote Similarity NPC111536
0.5147 Remote Similarity NPC76128
0.5094 Remote Similarity NPC142319
0.5088 Remote Similarity NPC80098
0.5082 Remote Similarity NPC479029
0.5077 Remote Similarity NPC146803
0.5077 Remote Similarity NPC604892
0.5075 Remote Similarity NPC271385
0.5075 Remote Similarity NPC605700

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC170953 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
0.5741 Remote Similarity NPD1091 Pre-clinical

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