Structure

Physi-Chem Properties

Molecular Weight:  155.07
Volume:  146.437
LogP:  -3.186
LogD:  -1.514
LogS:  -0.875
# Rotatable Bonds:  3
TPSA:  92.0
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.541
Synthetic Accessibility Score:  3.192
Fsp3:  0.333
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:  -5.56
MDCK Permeability:  2.077493627439253e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.067
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.86
Plasma Protein Binding (PPB):  8.2584228515625%
Volume Distribution (VD):  0.486
Pgp-substrate:  96.71338653564453%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.123
CYP2C19-inhibitor:  0.046
CYP2C19-substrate:  0.059
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.59
CYP2D6-inhibitor:  0.018
CYP2D6-substrate:  0.054
CYP3A4-inhibitor:  0.057
CYP3A4-substrate:  0.044

ADMET: Excretion

Clearance (CL):  9.116
Half-life (T1/2):  0.886

ADMET: Toxicity

hERG Blockers:  0.07
Human Hepatotoxicity (H-HT):  0.068
Drug-inuced Liver Injury (DILI):  0.027
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.164
Maximum Recommended Daily Dose:  0.019
Skin Sensitization:  0.815
Carcinogencity:  0.018
Eye Corrosion:  0.004
Eye Irritation:  0.086
Respiratory Toxicity:  0.098

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Similar NPs/Drugs  

  Natural Product: NPC94930

Natural Product ID:  NPC94930
Common Name*:   QZNNVYOVQUKYSC-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QZNNVYOVQUKYSC-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H9N3O2.ClH/c7-5(6(10)11)1-4-2-8-3-9-4;/h2-3,5H,1,7H2,(H,8,9)(H,10,11);1H
SMILES:  C(c1cnc[nH]1)C(C(=O)O)N.Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5351508
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:0004311] Histidine and derivatives

*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
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. DOI[10.1021/np960188t]
NPO7732 Solanum melongena Species Solanaceae Eukaryota n.a. root n.a. DOI[10.1271/bbb1961.42.623]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. PMID[16377847]
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. PMID[16595909]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[17841110]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO6715 Pseudostellaria heterophylla Species Caryophyllaceae Eukaryota n.a. root n.a. PMID[19157126]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[20778930]
NPO7732 Solanum melongena Species Solanaceae Eukaryota Roots n.a. n.a. PMID[31742403]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO6715 Pseudostellaria heterophylla Species Caryophyllaceae Eukaryota n.a. n.a. n.a. PMID[7673942]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. leaf n.a. PMID[9433811]
NPO7732 Solanum melongena Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7732 Solanum melongena Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7732 Solanum melongena Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO11969 Cyprinus carpio Species Cyprinidae Eukaryota n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Leaves n.a. Database[FooDB]
NPO7732 Solanum melongena Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6715 Pseudostellaria heterophylla Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7732 Solanum melongena Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11062 Euonymus grandiflorus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10713 Trifolium repens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11411 Gossypium herbaceum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29892.2 Musa paradisiaca var. sapientum Varieties Musaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30626 Trigonella foenum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11969 Cyprinus carpio Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4564 Anguilla japonica Species Anguillidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO7732 Solanum melongena Species Solanaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11062 Euonymus grandiflorus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10713 Trifolium repens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11411 Gossypium herbaceum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6715 Pseudostellaria heterophylla Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7732 Solanum melongena Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11969 Cyprinus carpio Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4564 Anguilla japonica Species Anguillidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11969 Cyprinus carpio Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10713 Trifolium repens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23017 Urtica dioica Species Urticaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7732 Solanum melongena Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6715 Pseudostellaria heterophylla Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11457 Chelidonium majus Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6715 Pseudostellaria heterophylla Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11600 Scolopendra subspinipes Species Scolopendridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6715 Pseudostellaria heterophylla Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7732 Solanum melongena Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11411 Gossypium herbaceum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11969 Cyprinus carpio Species Cyprinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4564 Anguilla japonica Species Anguillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11062 Euonymus grandiflorus Species Celastraceae 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

☑ 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 NPC94930 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 NPC94930 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