Structure

Physi-Chem Properties

Molecular Weight:  764.22
Volume:  709.147
LogP:  1.452
LogD:  0.926
LogS:  -3.23
# Rotatable Bonds:  15
TPSA:  279.05
# H-Bond Aceptor:  19
# H-Bond Donor:  8
# Rings:  5
# Heavy Atoms:  19

MedChem Properties

QED Drug-Likeness Score:  0.099
Synthetic Accessibility Score:  4.694
Fsp3:  0.429
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.68
MDCK Permeability:  5.584171231021173e-05
Pgp-inhibitor:  0.024
Pgp-substrate:  0.939
Human Intestinal Absorption (HIA):  0.939
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.111
Plasma Protein Binding (PPB):  81.03731536865234%
Volume Distribution (VD):  0.42
Pgp-substrate:  13.336600303649902%

ADMET: Metabolism

CYP1A2-inhibitor:  0.077
CYP1A2-substrate:  0.108
CYP2C19-inhibitor:  0.054
CYP2C19-substrate:  0.096
CYP2C9-inhibitor:  0.039
CYP2C9-substrate:  0.687
CYP2D6-inhibitor:  0.536
CYP2D6-substrate:  0.341
CYP3A4-inhibitor:  0.088
CYP3A4-substrate:  0.031

ADMET: Excretion

Clearance (CL):  5.878
Half-life (T1/2):  0.909

ADMET: Toxicity

hERG Blockers:  0.473
Human Hepatotoxicity (H-HT):  0.032
Drug-inuced Liver Injury (DILI):  0.598
AMES Toxicity:  0.112
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.278
Carcinogencity:  0.266
Eye Corrosion:  0.003
Eye Irritation:  0.252
Respiratory Toxicity:  0.004

Download Data

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

  Natural Product: NPC232854

Natural Product ID:  NPC232854
Common Name*:   MBYZKNWOAOHALV-HZGVNTEJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MBYZKNWOAOHALV-HZGVNTEJSA-N
Standard InCHI:  InChI=1S/C10H11NO3/c1-6-8-4-11-10(13)9(5-12)7(8)2-3-14-6/h4-6,9H,2-3H2,1H3/t6-,9-/m1/s1
SMILES:  C[C@@H]1C2=C(CCO1)[C@@H](C=O)C(=O)N=C2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans

*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
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. leaf n.a. PMID[21043460]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[21043460]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. stem n.a. PMID[21043460]
NPO27624 Swartzia simplex Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[26654828]
NPO12009 Abies pinsapo Species Pinaceae Eukaryota Wood n.a. n.a. PMID[7931362]
NPO18843 Antirrhinum majus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16073 Sarcomelicope megistophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19120 Strychnos aculeata Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16646 Artemisia campestris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17368 Erythrina senegalensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15856 Podocarpus hallii Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18843 Antirrhinum majus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16073 Sarcomelicope megistophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16646 Artemisia campestris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19120 Strychnos aculeata Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15856 Podocarpus hallii Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16817 Aglaia argentea Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17368 Erythrina senegalensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15856 Podocarpus hallii Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18843 Antirrhinum majus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16646 Artemisia campestris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17368 Erythrina senegalensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17711 Sphenoclea zeylanica Species Sphenocleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27624 Swartzia simplex Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16646 Artemisia campestris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16073 Sarcomelicope megistophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3046 Schisandra bicolor Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17493 Alstonia spatulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17054 Streptomyces gardneri Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17699 Solanum glaucophyllum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16958 Jurinea albicaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15518 Streptomyces netropsis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO18372 Lobophytum crassospiculatum Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18843 Antirrhinum majus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16817 Aglaia argentea Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13251 Iris nertchinskia Species Tarachodidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12009 Abies pinsapo Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14721 Dentitheca habereri Species Plumulariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19120 Strychnos aculeata Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15856 Podocarpus hallii Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18511 Latimeria chalumnae Species Coelacanthidae 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 NPC232854 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 NPC232854 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