Structure

Physi-Chem Properties

Molecular Weight:  241.13
Volume:  245.8
LogP:  1.814
LogD:  1.895
LogS:  -2.159
# Rotatable Bonds:  8
TPSA:  82.7
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.639
Synthetic Accessibility Score:  3.063
Fsp3:  0.583
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:  -4.571
MDCK Permeability:  1.5160538168856874e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.178
Human Intestinal Absorption (HIA):  0.038
20% Bioavailability (F20%):  0.014
30% Bioavailability (F30%):  0.195

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.994
Plasma Protein Binding (PPB):  88.44340515136719%
Volume Distribution (VD):  0.701
Pgp-substrate:  25.557369232177734%

ADMET: Metabolism

CYP1A2-inhibitor:  0.075
CYP1A2-substrate:  0.349
CYP2C19-inhibitor:  0.082
CYP2C19-substrate:  0.404
CYP2C9-inhibitor:  0.335
CYP2C9-substrate:  0.884
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.255
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.167

ADMET: Excretion

Clearance (CL):  14.258
Half-life (T1/2):  0.891

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.151
Drug-inuced Liver Injury (DILI):  0.15
AMES Toxicity:  0.035
Rat Oral Acute Toxicity:  0.612
Maximum Recommended Daily Dose:  0.049
Skin Sensitization:  0.521
Carcinogencity:  0.845
Eye Corrosion:  0.005
Eye Irritation:  0.068
Respiratory Toxicity:  0.403

Download Data

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

  Natural Product: NPC477642

Natural Product ID:  NPC477642
Common Name*:   3-oxo-N-(2-oxooxolan-3-yl)octanamide
IUPAC Name:   3-oxo-N-(2-oxooxolan-3-yl)octanamide
Synonyms:  
Standard InCHIKey:  FXCMGCFNLNFLSH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H19NO4/c1-2-3-4-5-9(14)8-11(15)13-10-6-7-17-12(10)16/h10H,2-8H2,1H3,(H,13,15)
SMILES:  CCCCCC(=O)CC(=O)NC1CCOC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   4476497
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0001189] N-acyl-alpha amino acids and derivatives

*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
NPO33619 Pantoea ananatis Species Erwiniaceae Bacteria n.a. n.a. n.a. PMID[18465897]

☑ 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
NPT314 Organism Bacillus cereus Bacillus cereus Activity = 62.5 ug/ml PMID[18465897]
NPT79 Organism Bacillus subtilis Bacillus subtilis Activity = 62.5 ug/ml PMID[18465897]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus Activity = 500 ug/ml PMID[18465897]

☑ 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 NPC477642 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
0.9697 High Similarity NPC477641
0.9697 High Similarity NPC477643
0.9697 High Similarity NPC320865
0.9062 High Similarity NPC145658
0.875 High Similarity NPC477644
0.7887 Intermediate Similarity NPC474299
0.7887 Intermediate Similarity NPC28348
0.7887 Intermediate Similarity NPC475808
0.7887 Intermediate Similarity NPC473985
0.7887 Intermediate Similarity NPC474298
0.7612 Intermediate Similarity NPC473599
0.7013 Intermediate Similarity NPC43219
0.6988 Remote Similarity NPC155670
0.6988 Remote Similarity NPC145748
0.6988 Remote Similarity NPC95478
0.6986 Remote Similarity NPC470108
0.6941 Remote Similarity NPC477728
0.6923 Remote Similarity NPC86064
0.6905 Remote Similarity NPC227051
0.6892 Remote Similarity NPC470109
0.6842 Remote Similarity NPC478256
0.68 Remote Similarity NPC470110
0.679 Remote Similarity NPC473984
0.6667 Remote Similarity NPC329181
0.6667 Remote Similarity NPC316242
0.6667 Remote Similarity NPC319110
0.6667 Remote Similarity NPC477730
0.6667 Remote Similarity NPC474312
0.662 Remote Similarity NPC254541
0.6585 Remote Similarity NPC315131
0.6585 Remote Similarity NPC315535
0.6585 Remote Similarity NPC478017
0.6543 Remote Similarity NPC472594
0.6517 Remote Similarity NPC477729
0.65 Remote Similarity NPC472595
0.6486 Remote Similarity NPC57420
0.6479 Remote Similarity NPC176164
0.6479 Remote Similarity NPC189301
0.6471 Remote Similarity NPC47135
0.6456 Remote Similarity NPC474403
0.641 Remote Similarity NPC476291
0.641 Remote Similarity NPC476285
0.6404 Remote Similarity NPC292345
0.6389 Remote Similarity NPC320598
0.6351 Remote Similarity NPC327252
0.6316 Remote Similarity NPC326651
0.6316 Remote Similarity NPC325117
0.6316 Remote Similarity NPC322319
0.6282 Remote Similarity NPC474812
0.625 Remote Similarity NPC141325
0.6222 Remote Similarity NPC322966
0.6173 Remote Similarity NPC476248
0.6173 Remote Similarity NPC138435
0.6154 Remote Similarity NPC159369
0.6154 Remote Similarity NPC39290
0.6129 Remote Similarity NPC226513
0.6119 Remote Similarity NPC227850
0.6092 Remote Similarity NPC469833
0.6092 Remote Similarity NPC469838
0.6087 Remote Similarity NPC322946
0.6081 Remote Similarity NPC17935
0.6076 Remote Similarity NPC314273
0.6076 Remote Similarity NPC193280
0.6061 Remote Similarity NPC52700
0.6061 Remote Similarity NPC145045
0.6061 Remote Similarity NPC105329
0.6061 Remote Similarity NPC63182
0.6056 Remote Similarity NPC471917
0.6056 Remote Similarity NPC322573
0.6044 Remote Similarity NPC193386
0.6024 Remote Similarity NPC476130
0.6024 Remote Similarity NPC476324
0.6022 Remote Similarity NPC208537
0.6022 Remote Similarity NPC270005
0.6 Remote Similarity NPC474833
0.6 Remote Similarity NPC263065
0.6 Remote Similarity NPC189178
0.5979 Remote Similarity NPC220234
0.597 Remote Similarity NPC289484
0.597 Remote Similarity NPC319709
0.5946 Remote Similarity NPC316826
0.5946 Remote Similarity NPC317143
0.5946 Remote Similarity NPC321536
0.5946 Remote Similarity NPC321468
0.5946 Remote Similarity NPC327748
0.5921 Remote Similarity NPC145627
0.5915 Remote Similarity NPC270041
0.5909 Remote Similarity NPC273545
0.589 Remote Similarity NPC317147
0.589 Remote Similarity NPC318260
0.5882 Remote Similarity NPC200618
0.5882 Remote Similarity NPC131770
0.5867 Remote Similarity NPC327170
0.5867 Remote Similarity NPC329564
0.5867 Remote Similarity NPC143722
0.5862 Remote Similarity NPC475542
0.5862 Remote Similarity NPC314466
0.5857 Remote Similarity NPC19576
0.5857 Remote Similarity NPC29950
0.5854 Remote Similarity NPC315897
0.5833 Remote Similarity NPC327831
0.5823 Remote Similarity NPC118524
0.5816 Remote Similarity NPC474952
0.5806 Remote Similarity NPC475801
0.5806 Remote Similarity NPC474593
0.5783 Remote Similarity NPC208657
0.5778 Remote Similarity NPC277918
0.5775 Remote Similarity NPC329495
0.5769 Remote Similarity NPC314103
0.5769 Remote Similarity NPC472609
0.5758 Remote Similarity NPC76051
0.5753 Remote Similarity NPC325985
0.5753 Remote Similarity NPC38463
0.575 Remote Similarity NPC469925
0.5745 Remote Similarity NPC474576
0.5733 Remote Similarity NPC319991
0.5732 Remote Similarity NPC33267
0.5732 Remote Similarity NPC324165
0.5732 Remote Similarity NPC170963
0.5732 Remote Similarity NPC114640
0.5732 Remote Similarity NPC126366
0.5732 Remote Similarity NPC169976
0.5714 Remote Similarity NPC470665
0.5714 Remote Similarity NPC327239
0.5714 Remote Similarity NPC90904
0.57 Remote Similarity NPC188453
0.57 Remote Similarity NPC42320
0.5694 Remote Similarity NPC321118
0.5694 Remote Similarity NPC316889
0.5692 Remote Similarity NPC53541
0.5684 Remote Similarity NPC315237
0.5684 Remote Similarity NPC471098
0.5684 Remote Similarity NPC62263
0.5684 Remote Similarity NPC173763
0.5676 Remote Similarity NPC278209
0.5673 Remote Similarity NPC67009
0.5663 Remote Similarity NPC55274
0.5652 Remote Similarity NPC106872
0.5644 Remote Similarity NPC301148
0.5644 Remote Similarity NPC124554
0.5644 Remote Similarity NPC5864
0.5641 Remote Similarity NPC316674
0.5616 Remote Similarity NPC53463
0.5616 Remote Similarity NPC320588
0.5616 Remote Similarity NPC23155
0.5616 Remote Similarity NPC469937
0.5612 Remote Similarity NPC134504
0.5612 Remote Similarity NPC47076
0.5606 Remote Similarity NPC176500

  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 NPC477642 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
0.9697 High Similarity NPD2256 Clinical (unspecified phase)
0.7656 Intermediate Similarity NPD9419 Clinical (unspecified phase)
0.6778 Remote Similarity NPD8394 Approved
0.6628 Remote Similarity NPD619 Phase 3
0.6585 Remote Similarity NPD7918 Clinical (unspecified phase)
0.6585 Remote Similarity NPD7917 Clinical (unspecified phase)
0.6494 Remote Similarity NPD3724 Clinical (unspecified phase)
0.6471 Remote Similarity NPD7345 Approved
0.6463 Remote Similarity NPD3160 Suspended
0.6456 Remote Similarity NPD6944 Clinical (unspecified phase)
0.6438 Remote Similarity NPD574 Approved
0.642 Remote Similarity NPD1453 Phase 1
0.6404 Remote Similarity NPD618 Clinical (unspecified phase)
0.6353 Remote Similarity NPD1448 Clinical (unspecified phase)
0.6351 Remote Similarity NPD575 Clinical (unspecified phase)
0.6329 Remote Similarity NPD9446 Approved
0.6264 Remote Similarity NPD4780 Clinical (unspecified phase)
0.6234 Remote Similarity NPD2263 Discontinued
0.6145 Remote Similarity NPD2689 Clinical (unspecified phase)
0.6087 Remote Similarity NPD9441 Phase 2
0.6061 Remote Similarity NPD1152 Phase 2
0.6044 Remote Similarity NPD4264 Clinical (unspecified phase)
0.6027 Remote Similarity NPD9433 Approved
0.6026 Remote Similarity NPD1429 Clinical (unspecified phase)
0.6024 Remote Similarity NPD11 Approved
0.6024 Remote Similarity NPD376 Approved
0.6 Remote Similarity NPD9204 Approved
0.6 Remote Similarity NPD9205 Approved
0.597 Remote Similarity NPD3211 Approved
0.5957 Remote Similarity NPD1447 Phase 3
0.5957 Remote Similarity NPD1446 Phase 3
0.5909 Remote Similarity NPD883 Phase 2
0.5909 Remote Similarity NPD882 Phase 2
0.5857 Remote Similarity NPD61 Approved
0.5857 Remote Similarity NPD8846 Approved
0.5857 Remote Similarity NPD8847 Approved
0.5854 Remote Similarity NPD1825 Clinical (unspecified phase)
0.5789 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5769 Remote Similarity NPD6413 Approved
0.5769 Remote Similarity NPD6941 Approved
0.5753 Remote Similarity NPD9659 Approved
0.5714 Remote Similarity NPD4283 Discontinued
0.5694 Remote Similarity NPD631 Approved
0.5694 Remote Similarity NPD630 Approved
0.5657 Remote Similarity NPD2255 Approved
0.5647 Remote Similarity NPD2257 Approved
0.5641 Remote Similarity NPD364 Discontinued
0.5638 Remote Similarity NPD3716 Discontinued
0.5625 Remote Similarity NPD886 Clinical (unspecified phase)
0.5616 Remote Similarity NPD3730 Approved
0.5616 Remote Similarity NPD3728 Approved
0.561 Remote Similarity NPD2694 Approved
0.561 Remote Similarity NPD8277 Approved
0.561 Remote Similarity NPD2696 Approved
0.561 Remote Similarity NPD2697 Approved
0.561 Remote Similarity NPD2695 Approved

  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