Structure

Physi-Chem Properties

Molecular Weight:  187.13
Volume:  192.222
LogP:  -3.251
LogD:  -0.853
LogS:  -1.527
# Rotatable Bonds:  7
TPSA:  99.2
# H-Bond Aceptor:  5
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.27
Synthetic Accessibility Score:  3.091
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.041
MDCK Permeability:  0.0022814078256487846
Pgp-inhibitor:  0.002
Pgp-substrate:  0.689
Human Intestinal Absorption (HIA):  0.249
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.633
Plasma Protein Binding (PPB):  6.029653549194336%
Volume Distribution (VD):  0.752
Pgp-substrate:  93.40522003173828%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.047
CYP2C19-inhibitor:  0.039
CYP2C19-substrate:  0.062
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.094
CYP2D6-inhibitor:  0.067
CYP2D6-substrate:  0.487
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.025

ADMET: Excretion

Clearance (CL):  8.607
Half-life (T1/2):  0.648

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.056
Drug-inuced Liver Injury (DILI):  0.008
AMES Toxicity:  0.029
Rat Oral Acute Toxicity:  0.069
Maximum Recommended Daily Dose:  0.012
Skin Sensitization:  0.223
Carcinogencity:  0.021
Eye Corrosion:  0.003
Eye Irritation:  0.066
Respiratory Toxicity:  0.363

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  Natural Product: NPC478850

Natural Product ID:  NPC478850
Common Name*:   ONYFNWIHJBLQKE-ZETCQYMHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ONYFNWIHJBLQKE-ZETCQYMHSA-N
Standard InCHI:  InChI=1S/C8H17N3O2/c1-6(9)11-5-3-2-4-7(10)8(12)13/h7H,2-5,10H2,1H3,(H2,9,11)(H,12,13)/t7-/m0/s1
SMILES:  CC(=N)NCCCC[C@@H](C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   2733506
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0002404] Alpha amino acids
                • [CHEMONTID:0004146] L-alpha-amino acids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[19053511]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[22372956]
NPO14197 Patrinia scabra Species Caprifoliaceae Eukaryota Roots n.a. n.a. PMID[23002924]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[27588583]
NPO14197 Patrinia scabra Species Caprifoliaceae Eukaryota Roots n.a. n.a. PMID[29799195]
NPO16444 Apios americana Species Fabaceae Eukaryota Tubers n.a. n.a. PMID[29932657]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[30724564]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14197 Patrinia scabra Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14197 Patrinia scabra Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16444 Apios americana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14197 Patrinia scabra Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21178 Chloranthus serratus Species Chloranthaceae 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 130.0 nM PMID[15163211]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens IC50 = 2400.0 nM PMID[15163211]
NPT3569 Individual Protein Nitric-oxide synthase, brain Homo sapiens IC50 = 1600.0 nM PMID[15163211]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 4600.0 nM PMID[8576908]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens IC50 = 138000.0 nM PMID[8576908]
NPT3569 Individual Protein Nitric-oxide synthase, brain Homo sapiens IC50 = 61000.0 nM PMID[8576908]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 4900.0 nM PMID[14761191]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens IC50 = 138000.0 nM PMID[14761191]
NPT3569 Individual Protein Nitric-oxide synthase, brain Homo sapiens IC50 = 35000.0 nM PMID[14761191]
NPT270 Individual Protein Nitric oxide synthase, inducible Mus musculus Ki = 2160.0 nM PMID[10843221]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 1400.0 nM PMID[10987430]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens IC50 = 7900.0 nM PMID[10987430]
NPT3569 Individual Protein Nitric-oxide synthase, brain Homo sapiens IC50 = 18400.0 nM PMID[10987430]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 130.0 nM PMID[11327580]
NPT269 Individual Protein Nitric-oxide synthase, brain Rattus norvegicus IC50 = 1600.0 nM PMID[11327580]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens IC50 = 2400.0 nM PMID[11327580]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 470000000.0 nM PMID[11327580]
NPT270 Individual Protein Nitric oxide synthase, inducible Mus musculus IC50 = 3300.0 nM PMID[7525961]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 100.0 nM PMID[12620067]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens IC50 = 2600.0 nM PMID[12620067]
NPT3569 Individual Protein Nitric-oxide synthase, brain Homo sapiens IC50 = 1500.0 nM PMID[12620067]
NPT579 Cell Line DLD-1 Homo sapiens IC50 = 2800.0 nM PMID[12620067]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 5000.0 nM PMID[9526553]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens IC50 = 38000.0 nM PMID[9526553]
NPT3569 Individual Protein Nitric-oxide synthase, brain Homo sapiens IC50 = 61000.0 nM PMID[9526553]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 2100.0 nM PMID[15357988]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens IC50 = 7900.0 nM PMID[15357988]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens Ratio = 3.7 uM PMID[15357988]
NPT3569 Individual Protein Nitric-oxide synthase, brain Homo sapiens IC50 = 17500.0 nM PMID[15357988]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 2100.0 nM PMID[15501067]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens IC50 = 7900.0 nM PMID[15501067]
NPT3569 Individual Protein Nitric-oxide synthase, brain Homo sapiens IC50 = 17500.0 nM PMID[15501067]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 280.0 nM PMID[18024030]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens IC50 = 2500.0 nM PMID[18024030]
NPT3569 Individual Protein Nitric-oxide synthase, brain Homo sapiens IC50 = 6000.0 nM PMID[18024030]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 31000.0 nM PMID[18024030]
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 18600.0 nM PMID[14510614]
NPT113 Cell Line RAW264.7 Mus musculus IC50 > 200000.0 nM PMID[14510614]
NPT113 Cell Line RAW264.7 Mus musculus Activity = 11.3 uM PMID[19500975]
NPT3517 Individual Protein Nitric oxide synthase, inducible Homo sapiens IC50 = 4677.35 nM PMID[21684157]
NPT3974 Individual Protein Nitric-oxide synthase, endothelial Homo sapiens IC50 > 100000.0 nM PMID[21684157]
NPT3569 Individual Protein Nitric-oxide synthase, brain Homo sapiens IC50 = 61659.5 nM PMID[21684157]
NPT113 Cell Line RAW264.7 Mus musculus Inhibition = 65.76 % PMID[24360561]
NPT113 Cell Line RAW264.7 Mus musculus Inhibition = 50.0 % PMID[24360561]
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 20140.0 nM PMID[24360561]
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 15800.0 nM PMID[25666824]
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 15800.0 nM PMID[29799195]
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 1550.0 nM PMID[29932657]
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 28290.0 nM PMID[29102229]
NPT113 Cell Line RAW264.7 Mus musculus Activity = 93.3 % PMID[30724564]
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 7000.0 nM PMID[30724564]
NPT113 Cell Line RAW264.7 Mus musculus Activity = 29.0 % PMID[31310917]
NPT113 Cell Line RAW264.7 Mus musculus Inhibition = 31.5 % PMID[31879211]
NPT15179 SINGLE PROTEIN Nitric oxide synthase, inducible Rattus norvegicus IC50 = 92000.0 nM PMID[7525961]
NPT29 Organism Rattus norvegicus Rattus norvegicus ID50 = 9.0 umol.kg-1 PMID[12620067]
NPT22974 SELECTIVITY GROUP Nitric oxide sythases; iNOS & nNOS Homo sapiens Ratio = 8.3 uM PMID[15357988]
NPT2 Others Unspecified Ratio IC50 = 9.0 n.a. PMID[18024030]
NPT22974 SELECTIVITY GROUP Nitric oxide sythases; iNOS & nNOS Homo sapiens Ratio IC50 = 21.0 n.a. PMID[18024030]
NPT317 Uncleic Acid Nucleic Acid Kd = 11000.0 nM PMID[17143270]
NPT2709 Organism Bacillus subtilis subsp. subtilis str. 168 Bacillus subtilis subsp. subtilis str. 168 MIC > 5000000.0 nM PMID[17143270]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 7500.0 nM PMID[27588583]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC478850 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC478850 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

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