Structure

Physi-Chem Properties

Molecular Weight:  211.17
Volume:  220.843
LogP:  2.269
LogD:  2.312
LogS:  -2.047
# Rotatable Bonds:  4
TPSA:  59.64
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.69
Synthetic Accessibility Score:  5.144
Fsp3:  0.909
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.709
MDCK Permeability:  1.352071194560267e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.996
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.021
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.585
Plasma Protein Binding (PPB):  59.94574737548828%
Volume Distribution (VD):  1.022
Pgp-substrate:  45.40023422241211%

ADMET: Metabolism

CYP1A2-inhibitor:  0.07
CYP1A2-substrate:  0.322
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.603
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.107
CYP2D6-inhibitor:  0.2
CYP2D6-substrate:  0.686
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.175

ADMET: Excretion

Clearance (CL):  9.763
Half-life (T1/2):  0.299

ADMET: Toxicity

hERG Blockers:  0.073
Human Hepatotoxicity (H-HT):  0.247
Drug-inuced Liver Injury (DILI):  0.255
AMES Toxicity:  0.905
Rat Oral Acute Toxicity:  0.814
Maximum Recommended Daily Dose:  0.557
Skin Sensitization:  0.422
Carcinogencity:  0.631
Eye Corrosion:  0.003
Eye Irritation:  0.022
Respiratory Toxicity:  0.946

Download Data

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

  Natural Product: NPC474467

Natural Product ID:  NPC474467
Common Name*:   Monanchoric Acid
IUPAC Name:   (1S,5R,7S)-7-pentyl-6-oxa-2,4-diazabicyclo[3.2.2]non-3-en-3-amine
Synonyms:   Monanchoric Acid
Standard InCHIKey:  RVYXBEHIFHTIKB-LPEHRKFASA-N
Standard InCHI:  InChI=1S/C11H21N3O/c1-2-3-4-5-9-8-6-7-10(15-9)14-11(12)13-8/h8-10H,2-7H2,1H3,(H3,12,13,14)/t8-,9-,10+/m0/s1
SMILES:  CCCCCC1C2CCC(O1)N=C(N2)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL469428
PubChem CID:   44559512
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000071] Diazepines
        • [CHEMONTID:0001337] 1,3-diazepines

*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
NPO32772 monanchora ungiculata Species Crambeidae Eukaryota n.a. n.a. n.a. PMID[15270573]

☑ 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 11.3 ug.mL-1 PMID[490329]

☑ 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 NPC474467 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
0.6071 Remote Similarity NPC208657
0.5922 Remote Similarity NPC166242
0.5922 Remote Similarity NPC92874
0.5922 Remote Similarity NPC322449
0.5922 Remote Similarity NPC62845
0.5922 Remote Similarity NPC189854
0.5865 Remote Similarity NPC325900
0.5865 Remote Similarity NPC10897
0.5825 Remote Similarity NPC314413
0.5825 Remote Similarity NPC314398
0.5825 Remote Similarity NPC239705
0.5783 Remote Similarity NPC268922
0.5663 Remote Similarity NPC471418
0.5647 Remote Similarity NPC306973
0.5647 Remote Similarity NPC476694
0.5647 Remote Similarity NPC476696
0.5647 Remote Similarity NPC476695

  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 NPC474467 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
0.6329 Remote Similarity NPD373 Approved
0.6329 Remote Similarity NPD374 Approved
0.5942 Remote Similarity NPD8793 Approved
0.5942 Remote Similarity NPD8792 Approved
0.5843 Remote Similarity NPD9429 Discontinued
0.5769 Remote Similarity NPD1155 Discontinued

  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