Natural Product: NPC232408

Natural Product IDNPC232408
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 3'-Dgtp
IUPAC Name [[(2S,4R,5R)-5-(2-amino-6-oxo-3H-purin-9-yl)-4-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] phosphono hydrogen phosphate
Synonyms 3'-dGTP
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL480707
PubChem CID 148770
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues
      • [CHEMONTID:0001506] Purine nucleotides
        • [CHEMONTID:0002134] Purine deoxyribonucleotides
          • [CHEMONTID:0002137] Purine deoxyribonucleoside triphosphates
            • [CHEMONTID:0002146] Purine 3'-deoxyribonucleoside triphosphates

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 QGYIFQKZZSSUCR-OBXARNEKSA-N
Standard InCHI InChI=1S/C10H16N5O13P3/c11-10-13-7-6(8(17)14-10)12-3-15(7)9-5(16)1-4(26-9)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-5,9,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,9+/m0/s1
SMILES C1[C@@H](COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O[C@H]([C@@H]1O)n1cnc2c1[nH]c(=N)nc2O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   507.0 Volume:   374.04
?
Van der Waals volume.
Dense:   1.355 LogP:   -4.054
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -1.627
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.275
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   19.0
TPSA:   279.86
?
Topological Polar Surface Area.
 H-Bond Acceptor:   18.0
H-Bond Donor:   8.0 Rings:   3.0
Heavy Atoms:   21.0

MedChem Properties

QED Drug-Likeness Score:   0.198 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.916 Fsp3:   0.5
MCE-18:   91.867
?
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:   0.092 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.024
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.048
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.407 Promiscuous compounds:   0.136

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.939 MDCK Permeability:   -4.972
Pgp-inhibitor:   0.0 Pgp-substrate:   0.0
PAMPA:   0.999
?
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):   0.303
20% Bioavailability (F20%):   0.0 30% Bioavailability (F30%):   0.588
50% Bioavailability (F50%):   0.335

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.607
Plasma Protein Binding (PPB):   22.12% Volume Distribution (VD):   -0.696
Fu: 66.8%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.452

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.015 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
HLM stability:   0.419
?
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):  1.581 Half-life (T1/2):  2.129

ADMET: Toxicity

hERG Blockers:  0.044 hERG Blockers (10um):  0.063
Human Hepatotoxicity (H-HT):  0.152 Drug-induced Liver Injury (DILI):  0.994
AMES Toxicity:  0.018 Rat Oral Acute Toxicity:  0.175
Maximum Recommended Daily Dose:  1.0 Skin Sensitization:  1.0
Carcinogencity:  0.881 Eye Corrosion:  0.0
Eye Irritation:  0.673 Respiratory Toxicity:  1.0
Drug-induced Neurotoxicity:  0.049 Ototoxicity:  0.004
Hematotoxicity:  0.007 Drug-induced Nephrotoxicity:  0.998
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.115
A549 Cytotoxicity:  0.002 Hek293 Cytotoxicity:  0.525
BCF:   -0.026
?
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:   2.337
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.504
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.474
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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
NPO11348 Cryptocarya chartacea Species Lauraceae Eukaryota n.a. trunk bark n.a. PMID[22050318]
NPO11348 Cryptocarya chartacea Species Lauraceae Eukaryota bark n.a. n.a. PMID[22050318]
NPO11348 Cryptocarya chartacea Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11348 Cryptocarya chartacea Species Lauraceae 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
NPT2 Others Unspecified n.a. IC50 = 20.0 nM PMID[17088479]
NPT2 Others Unspecified n.a. IC50 < 1000.0 nM PubChem BioAssay data set

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 NPC232408 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
0.7532 Intermediate Similarity NPC64705
0.7215 Intermediate Similarity NPC317746
0.6923 Remote Similarity NPC177169
0.6795 Remote Similarity NPC14590
0.6625 Remote Similarity NPC318590
0.6282 Remote Similarity NPC211820
0.625 Remote Similarity NPC89147
0.625 Remote Similarity NPC274384
0.6 Remote Similarity NPC186619
0.5526 Remote Similarity NPC61198
0.5349 Remote Similarity NPC481375
0.5063 Remote Similarity NPC262926

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC232408 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
0.5526 Remote Similarity NPD252 Clinical (unspecified phase)
0.5495 Remote Similarity NPD4074 Clinical (unspecified phase)
0.52 Remote Similarity NPD3086 Phase 3

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