Structure

Physi-Chem Properties

Molecular Weight:  250.12
Volume:  264.122
LogP:  3.445
LogD:  2.486
LogS:  -2.906
# Rotatable Bonds:  4
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.637
Synthetic Accessibility Score:  2.663
Fsp3:  0.357
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.675
MDCK Permeability:  1.4091655430092942e-05
Pgp-inhibitor:  0.023
Pgp-substrate:  0.019
Human Intestinal Absorption (HIA):  0.019
20% Bioavailability (F20%):  0.843
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.06
Plasma Protein Binding (PPB):  95.52935791015625%
Volume Distribution (VD):  0.886
Pgp-substrate:  6.529728889465332%

ADMET: Metabolism

CYP1A2-inhibitor:  0.951
CYP1A2-substrate:  0.865
CYP2C19-inhibitor:  0.663
CYP2C19-substrate:  0.212
CYP2C9-inhibitor:  0.598
CYP2C9-substrate:  0.869
CYP2D6-inhibitor:  0.839
CYP2D6-substrate:  0.397
CYP3A4-inhibitor:  0.415
CYP3A4-substrate:  0.207

ADMET: Excretion

Clearance (CL):  12.882
Half-life (T1/2):  0.568

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.271
Drug-inuced Liver Injury (DILI):  0.556
AMES Toxicity:  0.059
Rat Oral Acute Toxicity:  0.455
Maximum Recommended Daily Dose:  0.069
Skin Sensitization:  0.571
Carcinogencity:  0.078
Eye Corrosion:  0.005
Eye Irritation:  0.904
Respiratory Toxicity:  0.502

Download Data

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

  Natural Product: NPC28918

Natural Product ID:  NPC28918
Common Name*:   NYKKDRFAWMGIIT-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NYKKDRFAWMGIIT-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H18O4/c1-8(2)5-6-10-11(16)7-12(17)13(9(3)15)14(10)18-4/h5,7,16-17H,6H2,1-4H3
SMILES:  CC(=CCc1c(cc(c(C(=O)C)c1OC)O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   15558323
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003670] Aryl ketones
              • [CHEMONTID:0004296] Phenylketones
                • [CHEMONTID:0004298] Alkyl-phenylketones

*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
NPO25763 Miconia lepidota Species Melastomataceae Eukaryota n.a. n.a. n.a. PMID[11170656]
NPO25763 Miconia lepidota Species Melastomataceae Eukaryota n.a. Suriname rainforest n.a. PMID[11170656]
NPO40003 Acronychia pubescens Species Rutaceae Eukaryota Roots n.a. n.a. PMID[30865443]
NPO26697 Dracocephalum moldavicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23541 Smilax sieboldii Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26697 Dracocephalum moldavicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23541 Smilax sieboldii Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26697 Dracocephalum moldavicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23541 Smilax sieboldii Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23541 Smilax sieboldii Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26672 Matricaria tenuifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26697 Dracocephalum moldavicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24789 Opuntia elatior Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25724 Mya arenaria Species Myidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25763 Miconia lepidota Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25987 Euphorbia obtusifolia Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26734 Cupaniopsis azantha Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8394 Ramalina geniculata Species Ramalinaceae 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
NPT71 Cell Line HEK293 Homo sapiens GI = 79.1 % PMID[30865443]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 1800.0 nM PMID[30865443]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 3100.0 nM PMID[30865443]
NPT2 Others Unspecified Ratio IC50 = 1.7 n.a. PMID[30865443]

☑ 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 NPC28918 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 NPC28918 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