Structure

Physi-Chem Properties

Molecular Weight:  214.08
Volume:  209.002
LogP:  0.644
LogD:  -0.042
LogS:  -1.111
# Rotatable Bonds:  3
TPSA:  69.67
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.499
Synthetic Accessibility Score:  3.999
Fsp3:  0.7
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:  -5.038
MDCK Permeability:  5.8922327298205346e-05
Pgp-inhibitor:  0.222
Pgp-substrate:  0.053
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.094
30% Bioavailability (F30%):  0.114

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.958
Plasma Protein Binding (PPB):  19.862060546875%
Volume Distribution (VD):  0.745
Pgp-substrate:  80.951416015625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.103
CYP1A2-substrate:  0.326
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.539
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.06
CYP2D6-inhibitor:  0.09
CYP2D6-substrate:  0.073
CYP3A4-inhibitor:  0.036
CYP3A4-substrate:  0.218

ADMET: Excretion

Clearance (CL):  5.633
Half-life (T1/2):  0.635

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.888
Drug-inuced Liver Injury (DILI):  0.821
AMES Toxicity:  0.952
Rat Oral Acute Toxicity:  0.366
Maximum Recommended Daily Dose:  0.021
Skin Sensitization:  0.632
Carcinogencity:  0.923
Eye Corrosion:  0.993
Eye Irritation:  0.923
Respiratory Toxicity:  0.037

Download Data

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

  Natural Product: NPC216382

Natural Product ID:  NPC216382
Common Name*:   [(2R,3S,4S)-4-Acetyl-3,4-Dimethyl-5-Oxooxolan-2-Yl] Acetate
IUPAC Name:   [(2R,3S,4S)-4-acetyl-3,4-dimethyl-5-oxooxolan-2-yl] acetate
Synonyms:  
Standard InCHIKey:  OYMZTORLGBISLR-RHFNHBFPSA-N
Standard InCHI:  InChI=1S/C10H14O5/c1-5-8(14-7(3)12)15-9(13)10(5,4)6(2)11/h5,8H,1-4H3/t5-,8-,10+/m1/s1
SMILES:  C[C@@H]1[C@H](OC(=O)C)OC(=O)[C@]1(C)C(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL162264
PubChem CID:   100162
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001093] Carboxylic acid derivatives
          • [CHEMONTID:0001238] Carboxylic acid esters
            • [CHEMONTID:0003989] Acylals

*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
NPO6597 Inula spiraeifolia Species Asteraceae 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
NPT319 Cell Line B16 Mus musculus IC50 = 4000.0 nM PMID[505838]
NPT4526 Cell Line DA-3 cell line IC50 = 7000.0 nM PMID[505838]
NPT139 Cell Line HT-29 Homo sapiens IC50 = 5000.0 nM PMID[505838]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 6000.0 nM PMID[505838]
NPT32 Organism Mus musculus Mus musculus T1/2 < 0.08333 hr PMID[505838]

☑ 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 NPC216382 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
0.8519 High Similarity NPC233143
0.7419 Intermediate Similarity NPC220894
0.6364 Remote Similarity NPC325102
0.6329 Remote Similarity NPC25802
0.6329 Remote Similarity NPC51135
0.6329 Remote Similarity NPC82492
0.6329 Remote Similarity NPC101138
0.6316 Remote Similarity NPC282440
0.625 Remote Similarity NPC470243
0.6164 Remote Similarity NPC474755
0.6104 Remote Similarity NPC474754
0.6056 Remote Similarity NPC119838
0.6 Remote Similarity NPC179922
0.5902 Remote Similarity NPC305182
0.5857 Remote Similarity NPC157518
0.5857 Remote Similarity NPC306805
0.5857 Remote Similarity NPC215987
0.5857 Remote Similarity NPC295256
0.5849 Remote Similarity NPC321699
0.5833 Remote Similarity NPC221993
0.5823 Remote Similarity NPC1882
0.5797 Remote Similarity NPC268243
0.5775 Remote Similarity NPC473899
0.5769 Remote Similarity NPC469510
0.5763 Remote Similarity NPC308301
0.5741 Remote Similarity NPC14608
0.5682 Remote Similarity NPC41649
0.5672 Remote Similarity NPC132998
0.5663 Remote Similarity NPC478111
0.5652 Remote Similarity NPC306750
0.5641 Remote Similarity NPC70996
0.5636 Remote Similarity NPC316546
0.5634 Remote Similarity NPC469926
0.5634 Remote Similarity NPC476330
0.5625 Remote Similarity NPC60568
0.5606 Remote Similarity NPC198377

  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 NPC216382 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
0.6056 Remote Similarity NPD229 Approved
0.5857 Remote Similarity NPD9496 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