Structure

Physi-Chem Properties

Molecular Weight:  218.11
Volume:  219.467
LogP:  0.139
LogD:  0.641
LogS:  0.556
# Rotatable Bonds:  1
TPSA:  42.31
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.641
Synthetic Accessibility Score:  4.287
Fsp3:  0.5
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:  -4.843
MDCK Permeability:  1.2515723938122392e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.054
Human Intestinal Absorption (HIA):  0.65
20% Bioavailability (F20%):  0.301
30% Bioavailability (F30%):  0.716

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.851
Plasma Protein Binding (PPB):  27.70801544189453%
Volume Distribution (VD):  0.962
Pgp-substrate:  67.0469970703125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.322
CYP1A2-substrate:  0.246
CYP2C19-inhibitor:  0.191
CYP2C19-substrate:  0.468
CYP2C9-inhibitor:  0.171
CYP2C9-substrate:  0.222
CYP2D6-inhibitor:  0.261
CYP2D6-substrate:  0.705
CYP3A4-inhibitor:  0.083
CYP3A4-substrate:  0.261

ADMET: Excretion

Clearance (CL):  3.834
Half-life (T1/2):  0.507

ADMET: Toxicity

hERG Blockers:  0.044
Human Hepatotoxicity (H-HT):  0.331
Drug-inuced Liver Injury (DILI):  0.266
AMES Toxicity:  0.084
Rat Oral Acute Toxicity:  0.116
Maximum Recommended Daily Dose:  0.941
Skin Sensitization:  0.155
Carcinogencity:  0.875
Eye Corrosion:  0.005
Eye Irritation:  0.466
Respiratory Toxicity:  0.809

Download Data

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

  Natural Product: NPC86452

Natural Product ID:  NPC86452
Common Name*:   PCYQRXYBKKZUSR-ZJUUUORDSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PCYQRXYBKKZUSR-ZJUUUORDSA-N
Standard InCHI:  InChI=1S/C12H14N2O2/c15-8-13-5-9-4-10(7-13)11-2-1-3-12(16)14(11)6-9/h1-3,8-10H,4-7H2/t9-,10+/m1/s1
SMILES:  c1cc2[C@H]3C[C@H](CN(C3)C=O)Cn2c(=O)c1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1396784
PubChem CID:   6604689
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002719] Lupin alkaloids
        • [CHEMONTID:0002722] Cytisine 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
NPO24639 Streptomyces filamentosus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[17284073]
NPO546 Candida albicans Species Debaryomycetaceae Eukaryota n.a. n.a. n.a. PMID[23902158]
NPO11127 Inulanthera calva Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24639 Streptomyces filamentosus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15875 Scolopia chinensis Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7011 Chamomilla recutita n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO4061 Trollius europaeus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26656 Heliotropium hirsutissimum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO546 Candida albicans Species Debaryomycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12152 Nicotiana raimondii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9830 Arum maximum Species Araceae 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
NPT212 Individual Protein Cytochrome P450 2C9 Homo sapiens Potency = 31622.8 nM PMID[495200]

☑ 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 NPC86452 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
1.0 High Similarity NPC244256
0.9444 High Similarity NPC63284
0.9315 High Similarity NPC214125
0.9315 High Similarity NPC320667
0.8947 High Similarity NPC267203
0.8947 High Similarity NPC77890
0.8947 High Similarity NPC132858
0.8395 Intermediate Similarity NPC234822
0.8395 Intermediate Similarity NPC61321
0.8395 Intermediate Similarity NPC135639
0.8395 Intermediate Similarity NPC143344
0.8395 Intermediate Similarity NPC78058
0.7778 Intermediate Similarity NPC127430
0.7778 Intermediate Similarity NPC120699
0.7529 Intermediate Similarity NPC207048
0.7317 Intermediate Similarity NPC308050
0.7108 Intermediate Similarity NPC25513
0.6957 Remote Similarity NPC145707
0.6933 Remote Similarity NPC42477
0.6771 Remote Similarity NPC91036
0.6744 Remote Similarity NPC268580
0.6667 Remote Similarity NPC206660
0.6566 Remote Similarity NPC144714
0.6566 Remote Similarity NPC100810
0.6437 Remote Similarity NPC28529
0.6311 Remote Similarity NPC472856
0.6279 Remote Similarity NPC34672
0.6234 Remote Similarity NPC385
0.6203 Remote Similarity NPC477461
0.6203 Remote Similarity NPC477459
0.6154 Remote Similarity NPC133923
0.6019 Remote Similarity NPC143173
0.6 Remote Similarity NPC252684
0.5978 Remote Similarity NPC255430
0.5934 Remote Similarity NPC209232
0.5854 Remote Similarity NPC476559
0.5833 Remote Similarity NPC76869
0.5833 Remote Similarity NPC305602
0.5833 Remote Similarity NPC477460
0.5833 Remote Similarity NPC17497
0.573 Remote Similarity NPC281154
0.5679 Remote Similarity NPC470738
0.5657 Remote Similarity NPC473056
0.5625 Remote Similarity NPC231129

  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 NPC86452 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
0.8947 High Similarity NPD529 Approved
0.6707 Remote Similarity NPD815 Approved
0.6707 Remote Similarity NPD816 Approved
0.5926 Remote Similarity NPD4063 Clinical (unspecified phase)
0.5778 Remote Similarity NPD836 Clinical (unspecified phase)

  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