Structure

Physi-Chem Properties

Molecular Weight:  307.21
Volume:  338.149
LogP:  4.933
LogD:  4.755
LogS:  -4.021
# Rotatable Bonds:  11
TPSA:  63.33
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.473
Synthetic Accessibility Score:  3.088
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.638
MDCK Permeability:  2.323951957805548e-05
Pgp-inhibitor:  0.313
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.892
30% Bioavailability (F30%):  0.708

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.58
Plasma Protein Binding (PPB):  97.7076644897461%
Volume Distribution (VD):  1.752
Pgp-substrate:  1.582106351852417%

ADMET: Metabolism

CYP1A2-inhibitor:  0.61
CYP1A2-substrate:  0.388
CYP2C19-inhibitor:  0.797
CYP2C19-substrate:  0.335
CYP2C9-inhibitor:  0.923
CYP2C9-substrate:  0.98
CYP2D6-inhibitor:  0.021
CYP2D6-substrate:  0.107
CYP3A4-inhibitor:  0.276
CYP3A4-substrate:  0.182

ADMET: Excretion

Clearance (CL):  7.89
Half-life (T1/2):  0.802

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.914
Drug-inuced Liver Injury (DILI):  0.986
AMES Toxicity:  0.036
Rat Oral Acute Toxicity:  0.367
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.903
Carcinogencity:  0.569
Eye Corrosion:  0.111
Eye Irritation:  0.359
Respiratory Toxicity:  0.963

Download Data

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

  Natural Product: NPC477486

Natural Product ID:  NPC477486
Common Name*:   Lipoxazolidinone C
IUPAC Name:   (2E)-5-butyl-2-[(E)-4-methyl-2-oxodec-3-enylidene]-1,3-oxazolidin-4-one
Synonyms:   Lipoxazolidine C
Standard InCHIKey:  NHCONVHYGAHXRU-SWZGKVDCSA-N
Standard InCHI:  InChI=1S/C18H29NO3/c1-4-6-8-9-10-14(3)12-15(20)13-17-19-18(21)16(22-17)11-7-5-2/h12-13,16H,4-11H2,1-3H3,(H,19,21)/b14-12+,17-13+
SMILES:  CCCCCC/C(=C/C(=O)/C=C/1\NC(=O)C(O1)CCCC)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   23642823
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 = 4 ug/ml PMID[17845000]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 3 ug/ml PMID[17845000]
NPT1118 Organism Streptococcus pneumoniae Streptococcus pneumoniae MIC = 10 ug/ml PMID[17845000]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 2 ug/ml PMID[17845000]
NPT1122 Organism Haemophilus influenzae Haemophilus influenzae MIC = 16 ug/ml PMID[17845000]
NPT1122 Organism Haemophilus influenzae Haemophilus influenzae MIC = 5 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 NPC477486 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
1.0 High Similarity NPC477484
0.9726 High Similarity NPC477485
0.6705 Remote Similarity NPC477487
0.631 Remote Similarity NPC469836
0.6292 Remote Similarity NPC91332
0.6292 Remote Similarity NPC162741
0.6264 Remote Similarity NPC471595
0.625 Remote Similarity NPC20934
0.625 Remote Similarity NPC288381
0.6203 Remote Similarity NPC64971
0.618 Remote Similarity NPC471597
0.6163 Remote Similarity NPC288086
0.6163 Remote Similarity NPC469835
0.6154 Remote Similarity NPC469833
0.6154 Remote Similarity NPC326524
0.6154 Remote Similarity NPC329003
0.6154 Remote Similarity NPC325550
0.6154 Remote Similarity NPC469838
0.6098 Remote Similarity NPC83965
0.6092 Remote Similarity NPC217095
0.6092 Remote Similarity NPC264417
0.6026 Remote Similarity NPC321030
0.6 Remote Similarity NPC175614
0.5977 Remote Similarity NPC160540
0.5949 Remote Similarity NPC278202
0.5926 Remote Similarity NPC316674
0.5909 Remote Similarity NPC5485
0.5904 Remote Similarity NPC137163
0.59 Remote Similarity NPC189764
0.5897 Remote Similarity NPC192843
0.5897 Remote Similarity NPC281230
0.5889 Remote Similarity NPC474833
0.5882 Remote Similarity NPC471022
0.5882 Remote Similarity NPC103712
0.5882 Remote Similarity NPC291196
0.5844 Remote Similarity NPC242930
0.5811 Remote Similarity NPC225974
0.5804 Remote Similarity NPC7905
0.5804 Remote Similarity NPC315652
0.5789 Remote Similarity NPC217188
0.5784 Remote Similarity NPC265662
0.5783 Remote Similarity NPC176215
0.5783 Remote Similarity NPC296436
0.578 Remote Similarity NPC113012
0.578 Remote Similarity NPC122926
0.5769 Remote Similarity NPC313234
0.5765 Remote Similarity NPC249713
0.5765 Remote Similarity NPC474823
0.5765 Remote Similarity NPC310210
0.5761 Remote Similarity NPC472948
0.5752 Remote Similarity NPC59751
0.5752 Remote Similarity NPC27413
0.5752 Remote Similarity NPC271621
0.5745 Remote Similarity NPC144415
0.5745 Remote Similarity NPC228638
0.5743 Remote Similarity NPC233273
0.5743 Remote Similarity NPC205546
0.5743 Remote Similarity NPC50902
0.5733 Remote Similarity NPC261571
0.5714 Remote Similarity NPC469598
0.5714 Remote Similarity NPC159369
0.5714 Remote Similarity NPC39290
0.5701 Remote Similarity NPC201128
0.5701 Remote Similarity NPC154601
0.5701 Remote Similarity NPC271269
0.5699 Remote Similarity NPC280367
0.5698 Remote Similarity NPC280065
0.5698 Remote Similarity NPC94488
0.5698 Remote Similarity NPC236208
0.5698 Remote Similarity NPC45060
0.5698 Remote Similarity NPC262673
0.5698 Remote Similarity NPC475004
0.5684 Remote Similarity NPC477199
0.5682 Remote Similarity NPC314678
0.5679 Remote Similarity NPC130807
0.5667 Remote Similarity NPC301207
0.5658 Remote Similarity NPC188341
0.5658 Remote Similarity NPC49494
0.5657 Remote Similarity NPC166554
0.5652 Remote Similarity NPC291260
0.5648 Remote Similarity NPC251330
0.5647 Remote Similarity NPC473357
0.5647 Remote Similarity NPC193029
0.5647 Remote Similarity NPC243272
0.5644 Remote Similarity NPC70323
0.5644 Remote Similarity NPC3568
0.5644 Remote Similarity NPC23454
0.5644 Remote Similarity NPC192066
0.5644 Remote Similarity NPC35269
0.5644 Remote Similarity NPC256570
0.5644 Remote Similarity NPC473314
0.5644 Remote Similarity NPC17290
0.5644 Remote Similarity NPC262312
0.5641 Remote Similarity NPC281590
0.5638 Remote Similarity NPC65930
0.5638 Remote Similarity NPC473780
0.5638 Remote Similarity NPC73310
0.5638 Remote Similarity NPC473529
0.5638 Remote Similarity NPC180363
0.5638 Remote Similarity NPC145914
0.5638 Remote Similarity NPC11332
0.5638 Remote Similarity NPC474312
0.5638 Remote Similarity NPC473712
0.5638 Remote Similarity NPC131002
0.5638 Remote Similarity NPC329829
0.5638 Remote Similarity NPC475159
0.5638 Remote Similarity NPC94875
0.5632 Remote Similarity NPC94743
0.5632 Remote Similarity NPC318766
0.5632 Remote Similarity NPC477455
0.5632 Remote Similarity NPC291062
0.5625 Remote Similarity NPC325734
0.5619 Remote Similarity NPC175531
0.5618 Remote Similarity NPC474321
0.5614 Remote Similarity NPC476190
0.561 Remote Similarity NPC260573
0.561 Remote Similarity NPC29468
0.5607 Remote Similarity NPC472616
0.5604 Remote Similarity NPC474818
0.5604 Remote Similarity NPC49302
0.5604 Remote Similarity NPC176329
0.5604 Remote Similarity NPC51809
0.5604 Remote Similarity NPC125365
0.5603 Remote Similarity NPC473808
0.56 Remote Similarity NPC146852
0.56 Remote Similarity NPC472264

  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 NPC477486 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
0.6207 Remote Similarity NPD818 Approved
0.6207 Remote Similarity NPD819 Approved
0.5752 Remote Similarity NPD7505 Discontinued
0.5727 Remote Similarity NPD7116 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