Natural Product: NPC606116

Natural Product IDNPC606116
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 LMXOHSDXUQEUSF-YECHIGJVSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1214186
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 LMXOHSDXUQEUSF-YECHIGJVSA-N
Standard InCHI InChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
SMILES Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@@H](N)CC[C@H](N)C(=O)O)[C@@H](O)[C@H]1O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   381.18 Volume:   350.073
?
Van der Waals volume.
Dense:   1.089 LogP:   -2.639
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.327
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.278
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   16.0
TPSA:   208.65
?
Topological Polar Surface Area.
 H-Bond Acceptor:   12.0
H-Bond Donor:   9.0 Rings:   3.0
Heavy Atoms:   12.0

MedChem Properties

QED Drug-Likeness Score:   0.307 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.185 Fsp3:   0.6
MCE-18:   66.667
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.408 Fluc inhibitor:   0.016
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.042
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.01
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.015 Promiscuous compounds:   0.407

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.044 MDCK Permeability:   -5.444
Pgp-inhibitor:   0.0 Pgp-substrate:   0.703
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):   0.0
20% Bioavailability (F20%):   0.001 30% Bioavailability (F30%):   0.004
50% Bioavailability (F50%):   0.052

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.333
Plasma Protein Binding (PPB):   15.066% Volume Distribution (VD):   -0.49
Fu: 85.874%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.985
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:   0.097 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
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):  5.088 Half-life (T1/2):  1.501

ADMET: Toxicity

hERG Blockers:  0.047 hERG Blockers (10um):  0.122
Human Hepatotoxicity (H-HT):  0.75 Drug-induced Liver Injury (DILI):  0.597
AMES Toxicity:  0.669 Rat Oral Acute Toxicity:  0.587
Maximum Recommended Daily Dose:  0.169 Skin Sensitization:  0.986
Carcinogencity:  0.315 Eye Corrosion:  0.0
Eye Irritation:  0.026 Respiratory Toxicity:  0.633
Drug-induced Neurotoxicity:  0.981 Ototoxicity:  0.909
Hematotoxicity:  0.515 Drug-induced Nephrotoxicity:  0.94
Genotoxicity:  0.989 RPMI-8226 Immunitoxicity:  0.185
A549 Cytotoxicity:  0.067 Hek293 Cytotoxicity:  0.116
BCF:   0.06
?
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:   2.491
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.992
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.005
?
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
NPO50142 Streptomyces K05-0178 Genus Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO18488 Streptomyces griseolus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO48737 Streptomyces griseolus NRRL 37391 Genus Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO13840 Streptomyces incarnatus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO57371 Streptomyces incarnatus NRRL 8089 Genus Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO13840 Streptomyces incarnatus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO18488 Streptomyces griseolus Species Streptomycetaceae Bacteria 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
NPT1385 Individual protein Histone-lysine N-methyltransferase SETD7 Homo sapiens IC50 = 2500.0 nM PMID[20219369]
NPT2230 Individual protein Thiopurine S-methyltransferase Homo sapiens Kd = 10000.0 nM PMID[24913411]
NPT1385 Individual protein Histone-lysine N-methyltransferase SETD7 Homo sapiens Inhibition n.a. n.a. % PMID[23981144]
NPT5731 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 Homo sapiens IC50 = 28400.0 nM PMID[28739157]
NPT6098 Individual protein Histone-lysine N-methyltransferase, H3 lysine-79 specific Homo sapiens IC50 = 33710.0 nM PMID[29534934]
NPT29637 Single protein DNA adenine methylase Escherichia coli K-12 Inhibition n.a. n.a. % PMID[36581322]
NPT5731 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 Homo sapiens IC50 = 513000.0 nM PMID[24900829]
NPT28327 Single protein tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 Homo sapiens Inhibition = 70.2 % PMID[35849534]
NPT28821 Single protein mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase Homo sapiens Inhibition n.a. n.a. % PMID[36581322]
NPT4545 Individual protein Indolethylamine N-methyltransferase Homo sapiens IC50 = 4000.0 nM PMID[35904556]
NPT5731 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 Homo sapiens Inhibition = 100.0 % PMID[28739157]
NPT5731 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 Homo sapiens Inhibition n.a. n.a. % PMID[28739157]
NPT5731 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 Homo sapiens IC50 = 100.0 nM PMID[28739157]
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 4.11 % Identification of inhibitors of SARS-Cov2 M-Pro enzymatic activity using a small molecule repurposing screen
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 IC50 = 260.0 nM PMID[36097498]
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 4.76 % Identification of inhibitors of SARS-Cov2 M-Pro enzymatic activity using a small molecule repurposing screen
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 IC50 = 360.0 nM PMID[37192550]
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 IC50 = 278.0 nM PMID[38516599]
NPT4245 Individual protein Protein-arginine N-methyltransferase 1 Homo sapiens IC50 < 1000.0 nM PMID[20219369]
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 IC50 = 278.0 nM PMID[35439007]
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Activity = 0.0 % PMID[38516599]
NPT692 Individual protein Histone deacetylase 6 Homo sapiens Inhibition = -9.09 % HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators
NPT692 Individual protein Histone deacetylase 6 Homo sapiens Inhibition = -0.66 % HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 100.0 % PMID[35439007]
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 IC50 = 360.0 nM PMID[35439007]
NPT22367 Single protein Genome polyprotein Zika virus IC50 = 19200.0 nM PMID[36055002]
NPT5730 Individual protein Protein-beta-aspartate methyltransferase Homo sapiens Ki = 47000.0 nM PMID[1732534]
NPT5730 Individual protein Protein-beta-aspartate methyltransferase Homo sapiens Ki = 126000.0 nM PMID[1732534]
NPT29398 Single protein Histone-lysine N-methyltransferase NSD3 Homo sapiens IC50 = 61000.0 nM PMID[37182335]
NPT5 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens Inhibition n.a. n.a. % PMID[28739157]
NPT28739 Single protein RNA cytosine C(5)-methyltransferase NSUN2 Homo sapiens Inhibition = 77.1 % PMID[35849534]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens -TdeltaS = -4.8 kJ/mol PMID[35849534]
NPT5 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens IC50 = 509000.0 nM PMID[24900829]
NPT5 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens IC50 = 100.0 nM PMID[28739157]
NPT27471 Single protein mRNA cap guanine-N7 methyltransferase Homo sapiens IC50 = 0.55 nM PMID[33007557]
NPT6106 Individual protein Protein arginine N-methyltransferase 5 Homo sapiens IC50 = 8600.0 nM PMID[30366617]
NPT5 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens Inhibition = 43.0 % PMID[35849534]
NPT5 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens IC50 = 30100.0 nM PMID[28739157]
NPT25151 Single protein Nicotinamide N-methyltransferase Homo sapiens IC50 > 100000.0 nM PMID[35904556]
NPT28520 Single protein Glycine N-methyltransferase Homo sapiens IC50 = 316000.0 nM PMID[34257831]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens Kd = 20900.0 nM PMID[37312859]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens Activity n.a. n.a. n.a. PMID[37312859]
NPT27471 Single protein mRNA cap guanine-N7 methyltransferase Homo sapiens IC50 < 50.0 nM PMID[33007557]
NPT5 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens Inhibition = 79.5 % PMID[28739157]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens Inhibition n.a. n.a. % PMID[35849534]
NPT25907 Single protein NS5 Zika virus IC50 = 1620.0 nM PMID[31549836]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens IC50 = 13200.0 nM PMID[35849534]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens deltaH = -24.5 kJ/mol PMID[35849534]
NPT27471 Single protein mRNA cap guanine-N7 methyltransferase Homo sapiens Inhibition = 99.8 % PMID[32563813]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens Activity = 13.3 % PMID[37312859]
NPT25907 Single protein NS5 Zika virus IC50 = 1180.0 nM PMID[31549836]
NPT4675 Individual protein Histone-lysine N-methyltransferase NSD2 Homo sapiens IC50 = 46000.0 nM PMID[36863225]
NPT6108 Individual protein DNA (cytosine-5)-methyltransferase 3A Homo sapiens Inhibition = 98.0 % PMID[35849534]
NPT4675 Individual protein Histone-lysine N-methyltransferase NSD2 Homo sapiens IC50 = 79000.0 nM PMID[36642961]
NPT29857 Single protein Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific Homo sapiens IC50 = 46000.0 nM PMID[37182335]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens Inhibition = 83.5 % PMID[35849534]
NPT4675 Individual protein Histone-lysine N-methyltransferase NSD2 Homo sapiens IC50 = 79000.0 nM PMID[37182335]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens deltaG = -29.3 kJ/mol PMID[35849534]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens Inhibition = 94.0 % PMID[35849534]
NPT27471 Single protein mRNA cap guanine-N7 methyltransferase Homo sapiens IC50 = 5300.0 nM PMID[36958266]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens Activity n.a. n.a. n.a. PMID[35849534]
NPT29574 Single protein tRNA (cytosine(38)-C(5))-methyltransferase Homo sapiens Kd = 7500.0 nM PMID[35849534]
NPT27471 Single protein mRNA cap guanine-N7 methyltransferase Homo sapiens IC50 < 50.0 nM PMID[32563813]
NPT25151 Single protein Nicotinamide N-methyltransferase Homo sapiens Inhibition >= 50.0 % PMID[31265285]
NPT5 Individual protein Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 Homo sapiens IC50 = 30100.0 nM PMID[37974951]
NPT25151 Single protein Nicotinamide N-methyltransferase Homo sapiens IC50 = 12510.0 nM PMID[31265285]
NPT25151 Single protein Nicotinamide N-methyltransferase Homo sapiens IC50 = 5200.0 nM PMID[35904556]
NPT27134 Single protein Nonstructural protein 5 Dengue virus IC50 = 41.0 nM PMID[26771861]
NPT25151 Single protein Nicotinamide N-methyltransferase Homo sapiens IC50 = 3900.0 nM PMID[34458733]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT116 Cell line HL-60 Homo sapiens Inhibition = 41.0 % PMID[28739157]
NPT82 Cell line MDA-MB-231 Homo sapiens Inhibition = 42.8 % PMID[28739157]
NPT81 Cell line A549 Homo sapiens Activity > 95.0 % PMID[36097498]
NPT81 Cell line A549 Homo sapiens CC50 = 72930.0 nM PMID[34257831]
NPT71 Cell line HEK293 Homo sapiens CC50 > 500000.0 nM PMID[35849534]
NPT65 Cell line HepG2 Homo sapiens CC50 > 100000.0 nM PMID[34257831]
NPT28438 Unchecked Unchecked n.a. IC50 = 630.0 nM PMID[34273661]
NPT28438 Unchecked Unchecked n.a. IC50 = 360.0 nM PMID[32563813]
NPT28438 Unchecked Unchecked n.a. Inhibition n.a. n.a. % PMID[38242544]
NPT28438 Unchecked Unchecked n.a. IC50 = 30.0 nM PMID[26771861]
NPT28438 Unchecked Unchecked n.a. Kd = 136.0 nM PMID[26771861]
NPT28438 Unchecked Unchecked n.a. Inhibition n.a. n.a. % PMID[25909386]
NPT28438 Unchecked Unchecked n.a. IC50 = 1890.0 nM PMID[33007557]
NPT28438 Unchecked Unchecked n.a. Ratio = 6.0 n.a. PMID[26771861]
NPT28438 Unchecked Unchecked n.a. IC50 = 1180.0 nM PMID[34273661]
NPT28438 Unchecked Unchecked n.a. IC50 = 736.0 nM PMID[34257831]
NPT28438 Unchecked Unchecked n.a. IC50 = 41.0 nM PMID[33128910]
NPT28438 Unchecked Unchecked n.a. IC50 = 30.0 nM PMID[33128910]
NPT28438 Unchecked Unchecked n.a. IC50 = 160000.0 nM PMID[23981144]
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -0.06 % Cytopathic SARS-Cov2 screening on VERO-E6 cells in a large repurposing effort
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 2.28 % Identification of inhibitors of SARS-CoV-2 in-vitro cellular toxicity in human (Caco-2) cells using a large scale drug repurposing collection
NPT28438 Unchecked Unchecked n.a. Kd = 23000.0 nM PMID[36581322]
NPT28438 Unchecked Unchecked n.a. IC50 = 1900.0 nM PMID[33007557]
NPT28438 Unchecked Unchecked n.a. IC50 = 860.0 nM PMID[34257831]
NPT28438 Unchecked Unchecked n.a. Inhibition = 99.8 % PMID[32563813]
NPT28438 Unchecked Unchecked n.a. IC50 = 3400.0 nM PMID[38242544]
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 0.05 % Cytopathic SARS-Cov2 screening on VERO-E6 cells in a large repurposing effort
NPT28438 Unchecked Unchecked n.a. IC50 = 496.0 nM PMID[34257831]
NPT28438 Unchecked Unchecked n.a. Selectivity ratio = 2.0 n.a. PMID[35849534]
NPT28438 Unchecked Unchecked n.a. IC50 = 1180.0 nM PMID[36958266]
NPT28438 Unchecked Unchecked n.a. Delta Tm = 4.4 degrees C PMID[32563813]
NPT28438 Unchecked Unchecked n.a. Inhibition = 98.3 % PMID[32563813]
NPT28438 Unchecked Unchecked n.a. IC50 = 11000.0 nM PMID[23981144]
NPT28438 Unchecked Unchecked n.a. IC50 = 24000.0 nM PMID[36581322]
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition < 15.0 % PMID[36097498]
NPT28438 Unchecked Unchecked n.a. IC50 = 450.0 nM PMID[34257831]
NPT28438 Unchecked Unchecked n.a. Inhibition n.a. n.a. % PMID[36581322]
NPT28438 Unchecked Unchecked n.a. IC50 = 383.0 nM PMID[34257831]
NPT28438 Unchecked Unchecked n.a. IC50 = 112.0 nM PMID[34257831]
NPT28438 Unchecked Unchecked n.a. Ratio IC50 < 2.63 n.a. PMID[33007557]
NPT28438 Unchecked Unchecked n.a. IC50 = 1900.0 nM PMID[23981144]
NPT28438 Unchecked Unchecked n.a. IC50 = 1670.0 nM PMID[33007557]
NPT28438 Unchecked Unchecked n.a. IC50 = 1680.0 nM PMID[33007557]
NPT28438 Unchecked Unchecked n.a. Ratio IC50 = 0.32 n.a. PMID[33007557]
NPT28438 Unchecked Unchecked n.a. CC50 n.a. n.a. n.a. PMID[30170321]
NPT28438 Unchecked Unchecked n.a. CC50 = 99210.0 nM PMID[34257831]
NPT633 Organism Leishmania donovani Leishmania donovani Inhibition = 100.0 % PMID[1732534]
NPT633 Organism Leishmania donovani Leishmania donovani Inhibition = 88.0 % PMID[1732534]
NPT29846 Protein complex DNMT3A-DNMT3L Mus musculus Inhibition n.a. n.a. % PMID[36581322]
NPT22368 Organism Zika virus Zika virus IC50 > 50000.0 nM PMID[30170321]
NPT633 Organism Leishmania donovani Leishmania donovani IC50 = 1000.0 nM PMID[20185316]

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
Homo sapiens n.a. permeability n.a. n.a. n.a. PMID[34257831]





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference
- Mus musculus LD50 = 1000.0 mg/kg ToxVal

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 NPC606116 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
0.641 Remote Similarity NPC325906
0.6176 Remote Similarity NPC156461
0.6176 Remote Similarity NPC107374
0.6176 Remote Similarity NPC600382
0.6176 Remote Similarity NPC612067
0.6119 Remote Similarity NPC317821
0.5753 Remote Similarity NPC136349
0.5753 Remote Similarity NPC219313
0.5714 Remote Similarity NPC328479
0.5584 Remote Similarity NPC185991
0.5584 Remote Similarity NPC321814
0.5556 Remote Similarity NPC324484
0.5542 Remote Similarity NPC316618
0.5417 Remote Similarity NPC229974
0.5309 Remote Similarity NPC324198
0.5309 Remote Similarity NPC326529
0.5309 Remote Similarity NPC319100
0.5244 Remote Similarity NPC130586
0.5135 Remote Similarity NPC609472
0.5119 Remote Similarity NPC174802
0.5059 Remote Similarity NPC606410
0.5057 Remote Similarity NPC484199

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC606116 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
0.7568 Intermediate Similarity NPD1776 Approved
0.641 Remote Similarity NPD1777 Phase 4
0.6176 Remote Similarity NPD249 Phase 4
0.6176 Remote Similarity NPD250 Phase 4
0.5753 Remote Similarity NPD548 Clinical (unspecified phase)
0.5584 Remote Similarity NPD283 Phase 4
0.525 Remote Similarity NPD4171 Clinical (unspecified phase)
0.5122 Remote Similarity NPD338 Approved
0.5119 Remote Similarity NPD339 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