Structure

Physi-Chem Properties

Molecular Weight:  271.12
Volume:  269.332
LogP:  0.382
LogD:  0.9
LogS:  -2.698
# Rotatable Bonds:  0
TPSA:  61.72
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.612
Synthetic Accessibility Score:  5.472
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.906
MDCK Permeability:  5.081866220280062e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.013

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.986
Plasma Protein Binding (PPB):  17.790180206298828%
Volume Distribution (VD):  2.686
Pgp-substrate:  79.89263916015625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.122
CYP1A2-substrate:  0.388
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.778
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.155
CYP2D6-inhibitor:  0.692
CYP2D6-substrate:  0.877
CYP3A4-inhibitor:  0.043
CYP3A4-substrate:  0.458

ADMET: Excretion

Clearance (CL):  18.208
Half-life (T1/2):  0.376

ADMET: Toxicity

hERG Blockers:  0.244
Human Hepatotoxicity (H-HT):  0.014
Drug-inuced Liver Injury (DILI):  0.025
AMES Toxicity:  0.043
Rat Oral Acute Toxicity:  0.551
Maximum Recommended Daily Dose:  0.889
Skin Sensitization:  0.842
Carcinogencity:  0.067
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.71

Download Data

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

  Natural Product: NPC121485

Natural Product ID:  NPC121485
Common Name*:   DHMCGPVUHSTCIP-ONEGZZNKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DHMCGPVUHSTCIP-ONEGZZNKSA-N
Standard InCHI:  InChI=1S/C14H17NO4/c1-9(2)7-15-13(17)4-3-10-5-11(16)14-12(6-10)18-8-19-14/h3-6,9,16H,7-8H2,1-2H3,(H,15,17)/b4-3+
SMILES:  CC(C)CN=C(/C=C/c1cc(c2c(c1)OCO2)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   44513069
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000476] Cinnamic acids and derivatives
        • [CHEMONTID:0002810] Cinnamic acid amides

*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
NPO4756 Mesua elegans Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[20943395]
NPO5710 Michelia rajaniana Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[3236012]
NPO5060 Onychopetalum amazonicum Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9469 Digitalis obscura Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25530 Daphne blagayana Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29440 Sarcomyxa serotina Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4442 Artemisia austriaca Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO81 Erythrina orientalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3215 Phora atra Species Phoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5710 Michelia rajaniana Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9318 Stevia serrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4756 Mesua elegans Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO924 Russula subnigricans Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28383 Vernonia tufnellae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11244 Chrysolaena propinqua Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12990 Umbelopsis vinacea Species Umbelopsidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8378 Fagara heitzii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6557 Lotus villosus Species Fabaceae 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 NPC121485 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 NPC121485 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