Natural Product: NPC117529

Natural Product IDNPC117529
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 IQFYYKKMVGJFEH-CKHMMZHJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11085982
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues
      • [CHEMONTID:0000480] Pyrimidine nucleosides
        • [CHEMONTID:0002180] Pyrimidine 2'-deoxyribonucleosides

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 IQFYYKKMVGJFEH-CKHMMZHJSA-N
Standard InCHI InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1/i6D
SMILES Cc1cn([C@H]2C[C@@]([C@@H](CO)O2)(O)[2H])c(=O)nc1O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   243.1 Volume:   222.439
?
Van der Waals volume.
Dense:   1.093 LogP:   -0.791
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.269
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.84
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   12.0
TPSA:   104.81
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   3.0 Rings:   2.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.609 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.577 Fsp3:   0.6
MCE-18:   52.5
?
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:   0.098 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.027
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.019
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.046 Promiscuous compounds:   0.398

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.344 MDCK Permeability:   -4.83
Pgp-inhibitor:   0.0 Pgp-substrate:   0.0
PAMPA:   0.965
?
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):   0.0
20% Bioavailability (F20%):   0.056 30% Bioavailability (F30%):   0.024
50% Bioavailability (F50%):   0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.999
Plasma Protein Binding (PPB):   9.15% Volume Distribution (VD):   0.082
Fu: 90.183%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.117
OATP1B3 inhibitor:   0.072 BCRP inhibitor:   0.0
BSEP inhibitor:   0.353

ADMET: Metabolism

CYP1A2-inhibitor:   0.636 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.981 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.136 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.411 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
HLM stability:   0.006
?
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):  4.872 Half-life (T1/2):  1.473

ADMET: Toxicity

hERG Blockers:  0.072 hERG Blockers (10um):  0.236
Human Hepatotoxicity (H-HT):  0.921 Drug-induced Liver Injury (DILI):  0.944
AMES Toxicity:  0.603 Rat Oral Acute Toxicity:  0.199
Maximum Recommended Daily Dose:  0.575 Skin Sensitization:  0.999
Carcinogencity:  0.73 Eye Corrosion:  0.0
Eye Irritation:  0.306 Respiratory Toxicity:  0.322
Drug-induced Neurotoxicity:  0.884 Ototoxicity:  0.901
Hematotoxicity:  0.382 Drug-induced Nephrotoxicity:  0.96
Genotoxicity:  0.994 RPMI-8226 Immunitoxicity:  0.09
A549 Cytotoxicity:  0.37 Hek293 Cytotoxicity:  0.622
BCF:   0.164
?
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:   2.631
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.193
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.186
?
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
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.phytochem.2005.10.025]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. fruit body n.a. PMID[11520245]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. PMID[12045343]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. PMID[14695801]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. PMID[1791484]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. spore n.a. PMID[18827358]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota fruiting bodies Nagano, Japan 2008-MAY PMID[20039640]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. PMID[20384295]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota fruiting bodies n.a. n.a. PMID[20702092]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. seed n.a. PMID[21049975]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. PMID[21625478]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota fruiting bodies n.a. n.a. PMID[21924611]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. PMID[22014750]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. fruit body n.a. PMID[22044278]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota fruiting body n.a. n.a. PMID[22047696]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. aerial part n.a. PMID[25154406]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. PMID[26222905]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[30551419]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[35999251]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36432786]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36840093]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37653914]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38592874]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38719900]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[39065713]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[39683666]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. fruit body n.a. PMID[9635497]
NPO28669 Cuscuta australis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24062 Radix pseudostellariae Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28669 Cuscuta australis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29385 Nidus vespae n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO24062 Radix pseudostellariae Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29385 Nidus vespae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28669 Cuscuta australis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21460 Anethum graveolens Species Apiaceae 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]
NPO28669 Cuscuta australis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14347 Fritillaria anhuiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22292 Fritillaria przewalskii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28669 Cuscuta australis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5648 Fritillaria ussuriensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25269 Ganoderma lucidum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19581 Marchantia polymorpha Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21460 Anethum graveolens Species Apiaceae 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 NPC117529 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
0.6731 Remote Similarity NPC71339
0.6429 Remote Similarity NPC171116
0.6034 Remote Similarity NPC478793
0.5926 Remote Similarity NPC163352
0.5926 Remote Similarity NPC210456
0.5323 Remote Similarity NPC327344

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC117529 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
0.6731 Remote Similarity NPD280 Phase 4
0.6604 Remote Similarity NPD238 Clinical (unspecified phase)
0.6604 Remote Similarity NPD239 Phase 2
0.6034 Remote Similarity NPD251 Phase 4
0.5926 Remote Similarity NPD205 Phase 4
0.5614 Remote Similarity NPD240 Phase 3
0.5345 Remote Similarity NPD841 Phase 2

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