Structure

Physi-Chem Properties

Molecular Weight:  237.14
Volume:  245.749
LogP:  0.732
LogD:  0.978
LogS:  -0.936
# Rotatable Bonds:  2
TPSA:  52.93
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.798
Synthetic Accessibility Score:  3.381
Fsp3:  0.538
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:  -5.047
MDCK Permeability:  1.1575353710213676e-05
Pgp-inhibitor:  0.008
Pgp-substrate:  0.814
Human Intestinal Absorption (HIA):  0.094
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.623

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.398
Plasma Protein Binding (PPB):  47.815635681152344%
Volume Distribution (VD):  1.894
Pgp-substrate:  56.73279571533203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.257
CYP1A2-substrate:  0.8
CYP2C19-inhibitor:  0.135
CYP2C19-substrate:  0.875
CYP2C9-inhibitor:  0.034
CYP2C9-substrate:  0.804
CYP2D6-inhibitor:  0.248
CYP2D6-substrate:  0.883
CYP3A4-inhibitor:  0.035
CYP3A4-substrate:  0.499

ADMET: Excretion

Clearance (CL):  9.294
Half-life (T1/2):  0.745

ADMET: Toxicity

hERG Blockers:  0.073
Human Hepatotoxicity (H-HT):  0.339
Drug-inuced Liver Injury (DILI):  0.436
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.388
Maximum Recommended Daily Dose:  0.044
Skin Sensitization:  0.06
Carcinogencity:  0.03
Eye Corrosion:  0.012
Eye Irritation:  0.047
Respiratory Toxicity:  0.905

Download Data

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

  Natural Product: NPC102206

Natural Product ID:  NPC102206
Common Name*:   GJZNAEFHIYPPEM-HUXSOILUSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GJZNAEFHIYPPEM-HUXSOILUSA-N
Standard InCHI:  InChI=1S/C13H19NO3/c1-8-12(15)13(16)11(14(8)2)9-4-6-10(17-3)7-5-9/h4-8,11-13,15-16H,1-3H3/t8-,11-,12-,13-/m1/s1
SMILES:  C[C@@H]1[C@H]([C@@H]([C@@H](c2ccc(cc2)OC)N1C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10889945
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines
        • [CHEMONTID:0002336] Phenylpyrrolidines

*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
NPO17780 Curcuma heyneana Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[23387824]
NPO13153 Callicarpa macrophylla Species Lamiaceae Eukaryota Leaves n.a. n.a. PMID[26110519]
NPO13153 Callicarpa macrophylla Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11837 Codonopsis clematidea Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20907 Costus afer Species Costaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13153 Callicarpa macrophylla Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11837 Codonopsis clematidea Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3719 Potamophylax latipennis Species Limnephilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20907 Costus afer Species Costaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17627 Senecio rufus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16940 Phebalium ralstonii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15465 Mikania microptera Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17780 Curcuma heyneana Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10359 Chaiturus marrubiastrum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15038 Withania adpressa Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15789 Leucas cephalotes Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1547 Symphytum uplandicum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13153 Callicarpa macrophylla Species Lamiaceae 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
NPT20 Organism Candida albicans Candida albicans MIC > 1024.0 ug.mL-1 PMID[551660]
NPT747 Organism Acinetobacter baumannii Acinetobacter baumannii MIC > 1024.0 ug.mL-1 PMID[551660]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 1024.0 ug.mL-1 PMID[551660]
NPT172 Organism Proteus mirabilis Proteus mirabilis MIC = 128.0 ug.mL-1 PMID[551660]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC > 1024.0 ug.mL-1 PMID[551660]
NPT19 Organism Escherichia coli Escherichia coli MIC = 128.0 ug.mL-1 PMID[551660]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC <= 0.5 ug.mL-1 PMID[551660]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 32.0 mm PMID[551660]
NPT35 Others n.a. permeability = 100.0 % PMID[551660]
NPT35 Others n.a. permeability = 60.7 % PMID[551660]
NPT35 Others n.a. Activity = 93.3 % PMID[551660]
NPT35 Others n.a. Activity = 95.2 % PMID[551660]
NPT19 Organism Escherichia coli Escherichia coli MIC = 64.0 ug.mL-1 PMID[551660]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC = 1024.0 ug.mL-1 PMID[551660]
NPT172 Organism Proteus mirabilis Proteus mirabilis MIC = 64.0 ug.mL-1 PMID[551660]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 1024.0 ug.mL-1 PMID[551660]
NPT747 Organism Acinetobacter baumannii Acinetobacter baumannii MIC = 256.0 ug.mL-1 PMID[551660]

☑ 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 NPC102206 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 NPC102206 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