Structure

Physi-Chem Properties

Molecular Weight:  335.25
Volume:  372.741
LogP:  5.962
LogD:  5.18
LogS:  -4.459
# Rotatable Bonds:  13
TPSA:  63.33
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.38
Synthetic Accessibility Score:  3.026
Fsp3:  0.7
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.686
MDCK Permeability:  2.0055156710441224e-05
Pgp-inhibitor:  0.545
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.95
30% Bioavailability (F30%):  0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.484
Plasma Protein Binding (PPB):  98.35977935791016%
Volume Distribution (VD):  2.771
Pgp-substrate:  1.1892333030700684%

ADMET: Metabolism

CYP1A2-inhibitor:  0.532
CYP1A2-substrate:  0.292
CYP2C19-inhibitor:  0.798
CYP2C19-substrate:  0.178
CYP2C9-inhibitor:  0.92
CYP2C9-substrate:  0.984
CYP2D6-inhibitor:  0.029
CYP2D6-substrate:  0.085
CYP3A4-inhibitor:  0.459
CYP3A4-substrate:  0.148

ADMET: Excretion

Clearance (CL):  6.904
Half-life (T1/2):  0.723

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.912
Drug-inuced Liver Injury (DILI):  0.986
AMES Toxicity:  0.031
Rat Oral Acute Toxicity:  0.299
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.907
Carcinogencity:  0.485
Eye Corrosion:  0.098
Eye Irritation:  0.382
Respiratory Toxicity:  0.964

Download Data

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

  Natural Product: NPC477485

Natural Product ID:  NPC477485
Common Name*:   lipoxazolidinone B
IUPAC Name:   (2E)-2-[(E)-4-methyl-2-oxoundec-3-enylidene]-5-pentyl-1,3-oxazolidin-4-one
Synonyms:  
Standard InCHIKey:  IFYHOQUOFKVJCG-BIASGTOTSA-N
Standard InCHI:  InChI=1S/C20H33NO3/c1-4-6-8-9-11-12-16(3)14-17(22)15-19-21-20(23)18(24-19)13-10-7-5-2/h14-15,18H,4-13H2,1-3H3,(H,21,23)/b16-14+,19-15+
SMILES:  CCCCCCC/C(=C/C(=O)/C=C/1\NC(=O)C(O1)CCCCC)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   23642821
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
NPO33549 Marinispora sp. NPS008920 Species n.a. n.a. n.a. Cocos Lagoon, Guam 2002-JAN PMID[17845000]

☑ 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
NPT19 Organism Escherichia coli Escherichia coli MIC > 32 ug/ml PMID[17845000]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 6 ug/ml PMID[17845000]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 1.5 ug/ml PMID[17845000]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MIC = 1.3 ug/ml PMID[17845000]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MIC = 0.8 ug/ml PMID[17845000]
NPT1118 Organism Streptococcus pneumoniae Streptococcus pneumoniae MIC = 8 ug/ml PMID[17845000]
NPT1118 Organism Streptococcus pneumoniae Streptococcus pneumoniae MIC = 6 ug/ml PMID[17845000]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 3 ug/ml PMID[17845000]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 1.5 ug/ml PMID[17845000]
NPT1122 Organism Haemophilus influenzae Haemophilus influenzae MIC = 12 ug/ml PMID[17845000]
NPT1122 Organism Haemophilus influenzae Haemophilus influenzae MIC = 16 ug/ml PMID[17845000]

☑ 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 NPC477485 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
0.9726 High Similarity NPC477486
0.9726 High Similarity NPC477484
0.6742 Remote Similarity NPC477487
0.641 Remote Similarity NPC325550
0.641 Remote Similarity NPC326524
0.641 Remote Similarity NPC329003
0.6395 Remote Similarity NPC288086
0.6353 Remote Similarity NPC469836
0.6333 Remote Similarity NPC162741
0.6333 Remote Similarity NPC91332
0.6322 Remote Similarity NPC217095
0.6322 Remote Similarity NPC264417
0.6304 Remote Similarity NPC471595
0.6282 Remote Similarity NPC321030
0.625 Remote Similarity NPC64971
0.6207 Remote Similarity NPC469835
0.62 Remote Similarity NPC175614
0.6196 Remote Similarity NPC469838
0.6196 Remote Similarity NPC469833
0.6173 Remote Similarity NPC316674
0.6145 Remote Similarity NPC83965
0.6118 Remote Similarity NPC103712
0.6118 Remote Similarity NPC291196
0.6111 Remote Similarity NPC474833
0.6091 Remote Similarity NPC5485
0.6081 Remote Similarity NPC288381
0.6081 Remote Similarity NPC20934
0.6044 Remote Similarity NPC471597
0.6023 Remote Similarity NPC160540
0.6 Remote Similarity NPC278202
0.5982 Remote Similarity NPC315652
0.5982 Remote Similarity NPC7905
0.5978 Remote Similarity NPC472948
0.5963 Remote Similarity NPC122926
0.5963 Remote Similarity NPC113012
0.5957 Remote Similarity NPC144415
0.5952 Remote Similarity NPC137163
0.5949 Remote Similarity NPC192843
0.5949 Remote Similarity NPC281230
0.5941 Remote Similarity NPC189764
0.5929 Remote Similarity NPC27413
0.5929 Remote Similarity NPC271621
0.5929 Remote Similarity NPC59751
0.5921 Remote Similarity NPC188341
0.5921 Remote Similarity NPC49494
0.5918 Remote Similarity NPC159369
0.5918 Remote Similarity NPC39290
0.5905 Remote Similarity NPC469598
0.5897 Remote Similarity NPC242930
0.5895 Remote Similarity NPC477199
0.5888 Remote Similarity NPC154601
0.5888 Remote Similarity NPC271269
0.5882 Remote Similarity NPC193029
0.5882 Remote Similarity NPC473357
0.5862 Remote Similarity NPC477455
0.5862 Remote Similarity NPC94743
0.5862 Remote Similarity NPC291062
0.5851 Remote Similarity NPC180363
0.5851 Remote Similarity NPC65930
0.5851 Remote Similarity NPC73310
0.5851 Remote Similarity NPC473712
0.5851 Remote Similarity NPC145914
0.5851 Remote Similarity NPC329829
0.5851 Remote Similarity NPC131002
0.5851 Remote Similarity NPC473529
0.5851 Remote Similarity NPC475159
0.5851 Remote Similarity NPC94875
0.5851 Remote Similarity NPC474312
0.5851 Remote Similarity NPC473780
0.5851 Remote Similarity NPC11332
0.5843 Remote Similarity NPC474321
0.5842 Remote Similarity NPC192066
0.5842 Remote Similarity NPC3568
0.5842 Remote Similarity NPC17290
0.5842 Remote Similarity NPC256570
0.5833 Remote Similarity NPC296436
0.5833 Remote Similarity NPC251330
0.5833 Remote Similarity NPC176215
0.5825 Remote Similarity NPC265662
0.5814 Remote Similarity NPC249713
0.5814 Remote Similarity NPC263382
0.5814 Remote Similarity NPC125578
0.5814 Remote Similarity NPC146376
0.5814 Remote Similarity NPC474812
0.5806 Remote Similarity NPC47653
0.58 Remote Similarity NPC146852
0.5794 Remote Similarity NPC472616
0.5789 Remote Similarity NPC261571
0.5789 Remote Similarity NPC253801
0.5789 Remote Similarity NPC476190
0.5784 Remote Similarity NPC205546
0.5784 Remote Similarity NPC50902
0.5784 Remote Similarity NPC233273
0.5783 Remote Similarity NPC477707
0.578 Remote Similarity NPC140251
0.578 Remote Similarity NPC307903
0.5776 Remote Similarity NPC473808
0.5773 Remote Similarity NPC204686
0.5773 Remote Similarity NPC473687
0.5773 Remote Similarity NPC219498
0.5773 Remote Similarity NPC477010
0.5773 Remote Similarity NPC134807
0.5773 Remote Similarity NPC134885
0.5773 Remote Similarity NPC477015
0.5773 Remote Similarity NPC210218
0.5773 Remote Similarity NPC308412
0.575 Remote Similarity NPC52012
0.5747 Remote Similarity NPC280065
0.5747 Remote Similarity NPC94488
0.5747 Remote Similarity NPC16964
0.5747 Remote Similarity NPC45060
0.5747 Remote Similarity NPC471022
0.5747 Remote Similarity NPC475004
0.5747 Remote Similarity NPC262673
0.5743 Remote Similarity NPC61275
0.5741 Remote Similarity NPC472615
0.5741 Remote Similarity NPC201128
0.5739 Remote Similarity NPC296361
0.5732 Remote Similarity NPC130807
0.573 Remote Similarity NPC314678
0.5729 Remote Similarity NPC475706
0.5729 Remote Similarity NPC163093
0.5729 Remote Similarity NPC156804
0.5728 Remote Similarity NPC8098
0.5728 Remote Similarity NPC183449
0.5728 Remote Similarity NPC197294
0.5727 Remote Similarity NPC474725
0.5714 Remote Similarity NPC477457
0.5714 Remote Similarity NPC476269
0.5714 Remote Similarity NPC477012
0.5714 Remote Similarity NPC477456
0.5714 Remote Similarity NPC472614
0.5701 Remote Similarity NPC474563
0.57 Remote Similarity NPC166554
0.5698 Remote Similarity NPC472266
0.5698 Remote Similarity NPC243272
0.5698 Remote Similarity NPC127091
0.5698 Remote Similarity NPC22101
0.5698 Remote Similarity NPC148192
0.5698 Remote Similarity NPC473752
0.5698 Remote Similarity NPC104537
0.5698 Remote Similarity NPC271921
0.5698 Remote Similarity NPC330426
0.5696 Remote Similarity NPC281590
0.5686 Remote Similarity NPC23454
0.5686 Remote Similarity NPC473314
0.5686 Remote Similarity NPC35269
0.5686 Remote Similarity NPC70323
0.5686 Remote Similarity NPC262312
0.5686 Remote Similarity NPC477241
0.5682 Remote Similarity NPC42526
0.5679 Remote Similarity NPC325734
0.567 Remote Similarity NPC473669
0.567 Remote Similarity NPC235809
0.567 Remote Similarity NPC470400
0.567 Remote Similarity NPC477014
0.567 Remote Similarity NPC100921
0.567 Remote Similarity NPC103284
0.567 Remote Similarity NPC39167
0.567 Remote Similarity NPC292809
0.567 Remote Similarity NPC132496
0.567 Remote Similarity NPC329615
0.567 Remote Similarity NPC25764
0.567 Remote Similarity NPC110710
0.567 Remote Similarity NPC475268
0.567 Remote Similarity NPC322529
0.567 Remote Similarity NPC77871
0.567 Remote Similarity NPC9678
0.567 Remote Similarity NPC286338
0.567 Remote Similarity NPC473651
0.567 Remote Similarity NPC39279
0.567 Remote Similarity NPC82795
0.567 Remote Similarity NPC1083
0.567 Remote Similarity NPC473478
0.567 Remote Similarity NPC319036
0.567 Remote Similarity NPC231009
0.567 Remote Similarity NPC477018
0.567 Remote Similarity NPC120398
0.567 Remote Similarity NPC107986
0.567 Remote Similarity NPC283085
0.567 Remote Similarity NPC66346
0.567 Remote Similarity NPC223871
0.567 Remote Similarity NPC182383
0.567 Remote Similarity NPC329838
0.567 Remote Similarity NPC473156
0.567 Remote Similarity NPC202055
0.567 Remote Similarity NPC477013
0.567 Remote Similarity NPC471567
0.567 Remote Similarity NPC473671
0.5667 Remote Similarity NPC227396
0.5667 Remote Similarity NPC264178
0.5663 Remote Similarity NPC321838
0.5663 Remote Similarity NPC29468
0.566 Remote Similarity NPC313234
0.5658 Remote Similarity NPC225974
0.5652 Remote Similarity NPC474818
0.5652 Remote Similarity NPC51809
0.5652 Remote Similarity NPC125365
0.5652 Remote Similarity NPC176329
0.5652 Remote Similarity NPC49302

  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 NPC477485 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
0.625 Remote Similarity NPD818 Approved
0.625 Remote Similarity NPD819 Approved
0.5929 Remote Similarity NPD7505 Discontinued
0.5909 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5625 Remote Similarity NPD7601 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