Structure

Physi-Chem Properties

Molecular Weight:  114.08
Volume:  114.627
LogP:  -0.138
LogD:  -0.315
LogS:  0.651
# Rotatable Bonds:  1
TPSA:  46.33
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.479
Synthetic Accessibility Score:  1.848
Fsp3:  0.8
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:  -4.713
MDCK Permeability:  9.250426228391007e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.034
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.994
Plasma Protein Binding (PPB):  11.92446231842041%
Volume Distribution (VD):  1.149
Pgp-substrate:  80.90145874023438%

ADMET: Metabolism

CYP1A2-inhibitor:  0.085
CYP1A2-substrate:  0.378
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.158
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.157
CYP2D6-inhibitor:  0.037
CYP2D6-substrate:  0.425
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.117

ADMET: Excretion

Clearance (CL):  7.234
Half-life (T1/2):  0.548

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.087
Drug-inuced Liver Injury (DILI):  0.078
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.071
Maximum Recommended Daily Dose:  0.046
Skin Sensitization:  0.261
Carcinogencity:  0.068
Eye Corrosion:  0.008
Eye Irritation:  0.603
Respiratory Toxicity:  0.07

Download Data

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General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC176455

Natural Product ID:  NPC176455
Common Name*:   LCDCPQHFCOBUEF-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LCDCPQHFCOBUEF-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H10N2O/c6-5(8)7-3-1-2-4-7/h1-4H2,(H2,6,8)
SMILES:  C1CCN(C1)C(=N)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   138335
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines
        • [CHEMONTID:0001903] Pyrrolidine carboxylic acids and derivatives
          • [CHEMONTID:0002256] Pyrrolidinecarboxamides

*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
NPO4817 Briareum excavatum Species Briareidae Eukaryota n.a. n.a. n.a. PMID[10096858]
NPO4817 Briareum excavatum Species Briareidae Eukaryota n.a. n.a. n.a. PMID[10543904]
NPO4817 Briareum excavatum Species Briareidae Eukaryota n.a. n.a. n.a. PMID[11277747]
NPO4817 Briareum excavatum Species Briareidae Eukaryota n.a. n.a. n.a. PMID[11720523]
NPO287 Wrightia javanica Species Apocynaceae Eukaryota n.a. leaf n.a. PMID[12808258]
NPO4817 Briareum excavatum Species Briareidae Eukaryota n.a. n.a. n.a. PMID[9599257]
NPO9047.1 Brassica rapa subsp. oleifera Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO287 Wrightia javanica Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5510 Lepidium draba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5510 Lepidium draba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9047.1 Brassica rapa subsp. oleifera Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8290 Mycena megaspora Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6725 Tulipa hybrid Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4191 Thermococcus acidaminovorans Species Thermococcaceae Archaea n.a. n.a. n.a. Database[UNPD]
NPO8123 Aplysina cavernicola Species Aplysinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2651 Ceroplastes floridensis Species Coccidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4817 Briareum excavatum Species Briareidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3266 Euryops sulcatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO287 Wrightia javanica Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9047.1 Brassica rapa subsp. oleifera Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1594 [enterobacter] aerogenes Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO27875 Fallopia convolvulus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1512 Cissampelos fasciculata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7223 Castela tortuosa Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3434 Thymus camphoratus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6901 Lophosoria quadripinnata Species Dicksoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5510 Lepidium draba Species Brassicaceae 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 NPC176455 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 NPC176455 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