Structure

Physi-Chem Properties

Molecular Weight:  255.22
Volume:  285.381
LogP:  6.056
LogD:  4.242
LogS:  -5.355
# Rotatable Bonds:  10
TPSA:  38.33
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.587
Synthetic Accessibility Score:  3.209
Fsp3:  0.933
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.673
MDCK Permeability:  2.4602502890047617e-05
Pgp-inhibitor:  0.23
Pgp-substrate:  0.347
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.945
30% Bioavailability (F30%):  0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.493
Plasma Protein Binding (PPB):  96.41927337646484%
Volume Distribution (VD):  1.024
Pgp-substrate:  2.5650370121002197%

ADMET: Metabolism

CYP1A2-inhibitor:  0.622
CYP1A2-substrate:  0.635
CYP2C19-inhibitor:  0.6
CYP2C19-substrate:  0.075
CYP2C9-inhibitor:  0.368
CYP2C9-substrate:  0.757
CYP2D6-inhibitor:  0.443
CYP2D6-substrate:  0.647
CYP3A4-inhibitor:  0.89
CYP3A4-substrate:  0.185

ADMET: Excretion

Clearance (CL):  4.273
Half-life (T1/2):  0.216

ADMET: Toxicity

hERG Blockers:  0.116
Human Hepatotoxicity (H-HT):  0.19
Drug-inuced Liver Injury (DILI):  0.455
AMES Toxicity:  0.132
Rat Oral Acute Toxicity:  0.339
Maximum Recommended Daily Dose:  0.038
Skin Sensitization:  0.869
Carcinogencity:  0.137
Eye Corrosion:  0.086
Eye Irritation:  0.581
Respiratory Toxicity:  0.82

Download Data

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

  Natural Product: NPC471917

Natural Product ID:  NPC471917
Common Name*:   Oxazolidinone
IUPAC Name:   (4S,5S)-4-methyl-5-undecyl-1,3-oxazolidin-2-one
Synonyms:  
Standard InCHIKey:  DNOOUEUMNMSIFA-KBPBESRZSA-N
Standard InCHI:  InChI=1S/C15H29NO2/c1-3-4-5-6-7-8-9-10-11-12-14-13(2)16-15(17)18-14/h13-14H,3-12H2,1-2H3,(H,16,17)/t13-,14-/m0/s1
SMILES:  CCCCCCCCCCCC1C(NC(=O)O1)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3298697
PubChem CID:   90683234
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002491] Azolidines
        • [CHEMONTID:0000108] Oxazolidines
          • [CHEMONTID:0000196] Oxazolidinones

*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
NPO33478 xiphophora chondrophylla Species Fucaceae Eukaryota n.a. New Zealand n.a. PMID[24856903]

☑ 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
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC >= 260000.0 nM PMID[519143]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv IC50 = 114000.0 nM PMID[519143]

☑ 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 NPC471917 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
0.7368 Intermediate Similarity NPC270041
0.6786 Remote Similarity NPC29222
0.6786 Remote Similarity NPC96966
0.6786 Remote Similarity NPC121062
0.6618 Remote Similarity NPC474812
0.661 Remote Similarity NPC123814
0.661 Remote Similarity NPC474322
0.6462 Remote Similarity NPC17455
0.6462 Remote Similarity NPC145627
0.6393 Remote Similarity NPC471442
0.6393 Remote Similarity NPC471423
0.6333 Remote Similarity NPC470664
0.6316 Remote Similarity NPC319709
0.6316 Remote Similarity NPC289484
0.6308 Remote Similarity NPC477644
0.619 Remote Similarity NPC471605
0.619 Remote Similarity NPC471443
0.619 Remote Similarity NPC8979
0.6143 Remote Similarity NPC473985
0.6143 Remote Similarity NPC28348
0.6143 Remote Similarity NPC474299
0.6143 Remote Similarity NPC474298
0.6143 Remote Similarity NPC475808
0.6056 Remote Similarity NPC327486
0.6056 Remote Similarity NPC327753
0.6056 Remote Similarity NPC477642
0.6056 Remote Similarity NPC223174
0.6027 Remote Similarity NPC43219
0.6 Remote Similarity NPC233364
0.6 Remote Similarity NPC471421
0.6 Remote Similarity NPC195165
0.6 Remote Similarity NPC319991
0.5968 Remote Similarity NPC277072
0.5968 Remote Similarity NPC178263
0.5946 Remote Similarity NPC86064
0.5942 Remote Similarity NPC474402
0.5909 Remote Similarity NPC319131
0.589 Remote Similarity NPC477641
0.589 Remote Similarity NPC320865
0.589 Remote Similarity NPC477643
0.589 Remote Similarity NPC474403
0.5857 Remote Similarity NPC59221
0.5846 Remote Similarity NPC302569
0.5846 Remote Similarity NPC168308
0.5844 Remote Similarity NPC474833
0.5802 Remote Similarity NPC476523
0.5775 Remote Similarity NPC254617
0.5775 Remote Similarity NPC171850
0.5775 Remote Similarity NPC266242
0.5775 Remote Similarity NPC74555
0.5775 Remote Similarity NPC306763
0.5753 Remote Similarity NPC477200
0.5738 Remote Similarity NPC329181
0.5738 Remote Similarity NPC319110
0.5714 Remote Similarity NPC241279
0.5694 Remote Similarity NPC473419
0.5694 Remote Similarity NPC475127
0.5694 Remote Similarity NPC475715
0.5692 Remote Similarity NPC293551
0.5652 Remote Similarity NPC471419
0.5652 Remote Similarity NPC145658
0.5652 Remote Similarity NPC163134
0.5641 Remote Similarity NPC150557
0.5641 Remote Similarity NPC316807
0.5634 Remote Similarity NPC184150
0.5634 Remote Similarity NPC141156
0.5625 Remote Similarity NPC470666
0.5616 Remote Similarity NPC478256
0.5616 Remote Similarity NPC473710
0.5616 Remote Similarity NPC163538
0.5616 Remote Similarity NPC115800
0.5616 Remote Similarity NPC475694

  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 NPC471917 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
0.661 Remote Similarity NPD3215 Phase 1
0.6552 Remote Similarity NPD3214 Discontinued
0.6324 Remote Similarity NPD5380 Approved
0.6316 Remote Similarity NPD3211 Approved
0.614 Remote Similarity NPD1152 Phase 2
0.6056 Remote Similarity NPD9445 Approved
0.6 Remote Similarity NPD903 Approved
0.589 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5789 Remote Similarity NPD9229 Approved
0.5676 Remote Similarity NPD3187 Discontinued
0.5625 Remote Similarity NPD1448 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