Structure

Physi-Chem Properties

Molecular Weight:  176.09
Volume:  178.721
LogP:  0.023
LogD:  0.357
LogS:  0.205
# Rotatable Bonds:  0
TPSA:  34.03
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.611
Synthetic Accessibility Score:  3.573
Fsp3:  0.5
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:  -4.861
MDCK Permeability:  3.3515386803628644e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.083

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.902
Plasma Protein Binding (PPB):  16.247169494628906%
Volume Distribution (VD):  2.083
Pgp-substrate:  79.88090515136719%

ADMET: Metabolism

CYP1A2-inhibitor:  0.035
CYP1A2-substrate:  0.111
CYP2C19-inhibitor:  0.035
CYP2C19-substrate:  0.839
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.106
CYP2D6-inhibitor:  0.337
CYP2D6-substrate:  0.514
CYP3A4-inhibitor:  0.058
CYP3A4-substrate:  0.386

ADMET: Excretion

Clearance (CL):  7.081
Half-life (T1/2):  0.324

ADMET: Toxicity

hERG Blockers:  0.088
Human Hepatotoxicity (H-HT):  0.397
Drug-inuced Liver Injury (DILI):  0.044
AMES Toxicity:  0.49
Rat Oral Acute Toxicity:  0.883
Maximum Recommended Daily Dose:  0.911
Skin Sensitization:  0.151
Carcinogencity:  0.418
Eye Corrosion:  0.004
Eye Irritation:  0.026
Respiratory Toxicity:  0.665

Download Data

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

  Natural Product: NPC25513

Natural Product ID:  NPC25513
Common Name*:   Cyfusine
IUPAC Name:   1,2,3,3a,4,9b-hexahydropyrrolo[3,4-a]indolizin-6-one
Synonyms:  
Standard InCHIKey:  CXOGMMQKRNROKJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H12N2O/c13-10-3-1-2-9-8-5-11-4-7(8)6-12(9)10/h1-3,7-8,11H,4-6H2
SMILES:  c1cc2C3CNCC3Cn2c(=O)c1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL404660
PubChem CID:   11708150
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000089] Pyridines and derivatives
        • [CHEMONTID:0002224] Hydropyridines
          • [CHEMONTID:0001160] Pyridinones

*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
NPO11889 Dendrobium chrysanthum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11889 Dendrobium chrysanthum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11889 Dendrobium chrysanthum Species Orchidaceae 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
NPT414 Individual Protein Neuronal acetylcholine receptor protein alpha-7 subunit Rattus norvegicus Ki > 500.0 nM PMID[565834]
NPT412 Protein Complex Neuronal acetylcholine receptor; alpha4/beta2 Rattus norvegicus Ki = 16.0 nM PMID[565834]
NPT411 Protein Complex Neuronal acetylcholine receptor; alpha3/beta4 Homo sapiens Ki > 500.0 nM PMID[565834]

☑ 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 NPC25513 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
0.8 Intermediate Similarity NPC132858
0.8 Intermediate Similarity NPC267203
0.8 Intermediate Similarity NPC77890
0.7284 Intermediate Similarity NPC63284
0.7195 Intermediate Similarity NPC320667
0.7195 Intermediate Similarity NPC214125
0.7108 Intermediate Similarity NPC244256
0.7108 Intermediate Similarity NPC86452
0.6667 Remote Similarity NPC385
0.6579 Remote Similarity NPC133923
0.6556 Remote Similarity NPC61321
0.6556 Remote Similarity NPC78058
0.6556 Remote Similarity NPC135639
0.6556 Remote Similarity NPC234822
0.6556 Remote Similarity NPC143344
0.641 Remote Similarity NPC252684
0.6282 Remote Similarity NPC470738
0.6076 Remote Similarity NPC42477
0.6 Remote Similarity NPC127430
0.6 Remote Similarity NPC472194
0.6 Remote Similarity NPC120699
0.5895 Remote Similarity NPC476141
0.5854 Remote Similarity NPC206660
0.5833 Remote Similarity NPC76869
0.5833 Remote Similarity NPC477460
0.5765 Remote Similarity NPC96272
0.5714 Remote Similarity NPC28529
0.5684 Remote Similarity NPC207048
0.5604 Remote Similarity NPC308050

  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 NPC25513 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
0.8 Intermediate Similarity NPD529 Approved
0.6117 Remote Similarity NPD2905 Discontinued
0.5979 Remote Similarity NPD1691 Clinical (unspecified phase)
0.5747 Remote Similarity NPD815 Approved
0.5747 Remote Similarity NPD816 Approved

  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