Structure

Physi-Chem Properties

Molecular Weight:  142.1
Volume:  153.312
LogP:  2.366
LogD:  1.999
LogS:  -2.451
# Rotatable Bonds:  3
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.561
Synthetic Accessibility Score:  2.852
Fsp3:  0.875
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.385
MDCK Permeability:  3.538805685820989e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.443
30% Bioavailability (F30%):  0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.993
Plasma Protein Binding (PPB):  34.530670166015625%
Volume Distribution (VD):  0.975
Pgp-substrate:  68.312744140625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.917
CYP1A2-substrate:  0.691
CYP2C19-inhibitor:  0.583
CYP2C19-substrate:  0.744
CYP2C9-inhibitor:  0.119
CYP2C9-substrate:  0.677
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.521
CYP3A4-inhibitor:  0.04
CYP3A4-substrate:  0.212

ADMET: Excretion

Clearance (CL):  9.929
Half-life (T1/2):  0.525

ADMET: Toxicity

hERG Blockers:  0.086
Human Hepatotoxicity (H-HT):  0.063
Drug-inuced Liver Injury (DILI):  0.052
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.041
Maximum Recommended Daily Dose:  0.055
Skin Sensitization:  0.828
Carcinogencity:  0.508
Eye Corrosion:  0.934
Eye Irritation:  0.985
Respiratory Toxicity:  0.31

Download Data

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

  Natural Product: NPC282440

Natural Product ID:  NPC282440
Common Name*:   Gama-Octalactone
IUPAC Name:   3-butyloxolan-2-one
Synonyms:   Gama-Octalactone
Standard InCHIKey:  GNGUMAGSNTVFLB-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H14O2/c1-2-3-4-7-5-6-10-8(7)9/h7H,2-6H2,1H3
SMILES:  CCCCC1CCOC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL455439
PubChem CID:   86852
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[16562834]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. fruit n.a. PMID[24155209]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[24959987]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[25302569]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8187 Schisandra chinensis Species Schisandraceae 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
NPT1652 Individual Protein Serum paraoxonase/arylesterase 1 Homo sapiens Activity = 6.92 umol/min/mg PMID[488780]

☑ 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 NPC282440 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
0.913 High Similarity NPC305182
0.8261 Intermediate Similarity NPC308301
0.8085 Intermediate Similarity NPC249754
0.8043 Intermediate Similarity NPC273545
0.8 Intermediate Similarity NPC176500
0.7907 Intermediate Similarity NPC316546
0.7872 Intermediate Similarity NPC63182
0.7872 Intermediate Similarity NPC52700
0.7872 Intermediate Similarity NPC105329
0.7872 Intermediate Similarity NPC145045
0.7727 Intermediate Similarity NPC94368
0.7727 Intermediate Similarity NPC81263
0.7727 Intermediate Similarity NPC80234
0.7674 Intermediate Similarity NPC14608
0.7556 Intermediate Similarity NPC149299
0.7556 Intermediate Similarity NPC250028
0.7556 Intermediate Similarity NPC40597
0.7556 Intermediate Similarity NPC256163
0.7451 Intermediate Similarity NPC314084
0.7442 Intermediate Similarity NPC80641
0.7442 Intermediate Similarity NPC154642
0.7442 Intermediate Similarity NPC80396
0.7391 Intermediate Similarity NPC248763
0.7391 Intermediate Similarity NPC53541
0.7391 Intermediate Similarity NPC325452
0.7368 Intermediate Similarity NPC306750
0.7333 Intermediate Similarity NPC223249
0.7234 Intermediate Similarity NPC203531
0.7234 Intermediate Similarity NPC236579
0.7209 Intermediate Similarity NPC155872
0.7174 Intermediate Similarity NPC165533
0.7143 Intermediate Similarity NPC314679
0.7111 Intermediate Similarity NPC22903
0.7111 Intermediate Similarity NPC54980
0.7111 Intermediate Similarity NPC305660
0.7111 Intermediate Similarity NPC201622
0.7045 Intermediate Similarity NPC321699
0.7037 Intermediate Similarity NPC319589
0.7 Intermediate Similarity NPC157518
0.6977 Remote Similarity NPC286498
0.6977 Remote Similarity NPC154396
0.6977 Remote Similarity NPC57499
0.6957 Remote Similarity NPC219536
0.6957 Remote Similarity NPC3531
0.6957 Remote Similarity NPC31551
0.6939 Remote Similarity NPC287231
0.6939 Remote Similarity NPC47363
0.6939 Remote Similarity NPC55023
0.6897 Remote Similarity NPC478126
0.6889 Remote Similarity NPC252843
0.6863 Remote Similarity NPC324793
0.6863 Remote Similarity NPC477878
0.6863 Remote Similarity NPC13105
0.6818 Remote Similarity NPC289344
0.6818 Remote Similarity NPC301398
0.6818 Remote Similarity NPC156630
0.6818 Remote Similarity NPC223374
0.6818 Remote Similarity NPC196442
0.6818 Remote Similarity NPC86545
0.6809 Remote Similarity NPC12156
0.6809 Remote Similarity NPC161097
0.6809 Remote Similarity NPC28598
0.6744 Remote Similarity NPC178643
0.6744 Remote Similarity NPC322892
0.6744 Remote Similarity NPC286695
0.6744 Remote Similarity NPC35371
0.6744 Remote Similarity NPC168714
0.6744 Remote Similarity NPC41007
0.6735 Remote Similarity NPC317128
0.6721 Remote Similarity NPC295256
0.6721 Remote Similarity NPC469926
0.6667 Remote Similarity NPC21844
0.6667 Remote Similarity NPC326957
0.6667 Remote Similarity NPC21374
0.6667 Remote Similarity NPC82315
0.6604 Remote Similarity NPC142103
0.6562 Remote Similarity NPC5714
0.6562 Remote Similarity NPC295788
0.6562 Remote Similarity NPC144511
0.6562 Remote Similarity NPC296522
0.6562 Remote Similarity NPC199557
0.6557 Remote Similarity NPC314103
0.6545 Remote Similarity NPC72722
0.6522 Remote Similarity NPC128996
0.6512 Remote Similarity NPC40965
0.6512 Remote Similarity NPC12904
0.6508 Remote Similarity NPC469925
0.6481 Remote Similarity NPC274261
0.6481 Remote Similarity NPC291724
0.6471 Remote Similarity NPC30195
0.6471 Remote Similarity NPC12438
0.6462 Remote Similarity NPC472955
0.6444 Remote Similarity NPC218357
0.6441 Remote Similarity NPC472019
0.6441 Remote Similarity NPC226602
0.6441 Remote Similarity NPC470363
0.6441 Remote Similarity NPC472020
0.6415 Remote Similarity NPC26253
0.6415 Remote Similarity NPC250919
0.6415 Remote Similarity NPC476469
0.6406 Remote Similarity NPC119838
0.6364 Remote Similarity NPC170167
0.6364 Remote Similarity NPC216407
0.6364 Remote Similarity NPC163003
0.6364 Remote Similarity NPC129665
0.6364 Remote Similarity NPC470243
0.6349 Remote Similarity NPC135043
0.6349 Remote Similarity NPC315525
0.6349 Remote Similarity NPC84562
0.6333 Remote Similarity NPC472021
0.6316 Remote Similarity NPC216382
0.6308 Remote Similarity NPC28526
0.6304 Remote Similarity NPC155263
0.6296 Remote Similarity NPC55678
0.6269 Remote Similarity NPC269206
0.6269 Remote Similarity NPC473775
0.6269 Remote Similarity NPC472956
0.6269 Remote Similarity NPC473699
0.6269 Remote Similarity NPC474100
0.6269 Remote Similarity NPC51249
0.6269 Remote Similarity NPC58956
0.6269 Remote Similarity NPC475260
0.6269 Remote Similarity NPC295633
0.6269 Remote Similarity NPC475232
0.6269 Remote Similarity NPC474755
0.6269 Remote Similarity NPC109510
0.625 Remote Similarity NPC279026
0.625 Remote Similarity NPC301585
0.625 Remote Similarity NPC201844
0.625 Remote Similarity NPC261080
0.625 Remote Similarity NPC14227
0.625 Remote Similarity NPC301696
0.625 Remote Similarity NPC469868
0.625 Remote Similarity NPC113928
0.625 Remote Similarity NPC154186
0.623 Remote Similarity NPC469922
0.6226 Remote Similarity NPC106872
0.62 Remote Similarity NPC325102
0.619 Remote Similarity NPC317739
0.619 Remote Similarity NPC281943
0.619 Remote Similarity NPC234005
0.619 Remote Similarity NPC215987
0.619 Remote Similarity NPC306805
0.6182 Remote Similarity NPC287811
0.6182 Remote Similarity NPC244452
0.6176 Remote Similarity NPC48641
0.6176 Remote Similarity NPC215030
0.6176 Remote Similarity NPC469643
0.6176 Remote Similarity NPC140287
0.6176 Remote Similarity NPC55508
0.6176 Remote Similarity NPC476355
0.6176 Remote Similarity NPC469641
0.6176 Remote Similarity NPC472966
0.6167 Remote Similarity NPC475821
0.6167 Remote Similarity NPC125506
0.6154 Remote Similarity NPC172042
0.6129 Remote Similarity NPC235788
0.6094 Remote Similarity NPC18252
0.6087 Remote Similarity NPC228411
0.6087 Remote Similarity NPC138408
0.6087 Remote Similarity NPC155587
0.6087 Remote Similarity NPC317203
0.6087 Remote Similarity NPC324762
0.6087 Remote Similarity NPC471491
0.6087 Remote Similarity NPC193351
0.6087 Remote Similarity NPC226669
0.6087 Remote Similarity NPC179922
0.6071 Remote Similarity NPC310746
0.6066 Remote Similarity NPC66145
0.6061 Remote Similarity NPC98711
0.6061 Remote Similarity NPC475062
0.6047 Remote Similarity NPC127696
0.6042 Remote Similarity NPC268826
0.6038 Remote Similarity NPC324004
0.6038 Remote Similarity NPC328497
0.6034 Remote Similarity NPC46151
0.6 Remote Similarity NPC216630
0.6 Remote Similarity NPC41017
0.6 Remote Similarity NPC99700
0.6 Remote Similarity NPC289388
0.6 Remote Similarity NPC92489
0.6 Remote Similarity NPC149184
0.6 Remote Similarity NPC266159
0.6 Remote Similarity NPC171736
0.6 Remote Similarity NPC123360
0.6 Remote Similarity NPC472967
0.6 Remote Similarity NPC196924
0.6 Remote Similarity NPC286842
0.6 Remote Similarity NPC235906
0.6 Remote Similarity NPC147054
0.6 Remote Similarity NPC108238
0.6 Remote Similarity NPC476601
0.6 Remote Similarity NPC472959
0.6 Remote Similarity NPC209970
0.6 Remote Similarity NPC307783
0.6 Remote Similarity NPC175342
0.5968 Remote Similarity NPC253204
0.5968 Remote Similarity NPC10659
0.5965 Remote Similarity NPC233143
0.5957 Remote Similarity NPC134782

  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 NPC282440 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
0.8095 Intermediate Similarity NPD9449 Clinical (unspecified phase)
0.7619 Intermediate Similarity NPD9447 Approved
0.7143 Intermediate Similarity NPD634 Phase 3
0.6957 Remote Similarity NPD77 Approved
0.6957 Remote Similarity NPD9450 Approved
0.6939 Remote Similarity NPD2699 Approved
0.6875 Remote Similarity NPD387 Clinical (unspecified phase)
0.6863 Remote Similarity NPD2266 Phase 2
0.6721 Remote Similarity NPD9496 Clinical (unspecified phase)
0.6538 Remote Similarity NPD6125 Clinical (unspecified phase)
0.6458 Remote Similarity NPD9635 Discontinued
0.6441 Remote Similarity NPD3198 Approved
0.6429 Remote Similarity NPD615 Clinical (unspecified phase)
0.6406 Remote Similarity NPD229 Approved
0.6383 Remote Similarity NPD3206 Approved
0.6379 Remote Similarity NPD4279 Approved
0.6364 Remote Similarity NPD3186 Phase 1
0.625 Remote Similarity NPD9448 Phase 2
0.625 Remote Similarity NPD633 Phase 3
0.6167 Remote Similarity NPD4280 Approved
0.614 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6061 Remote Similarity NPD2696 Approved
0.6061 Remote Similarity NPD2694 Approved
0.6061 Remote Similarity NPD2697 Approved
0.6061 Remote Similarity NPD2695 Approved
0.6 Remote Similarity NPD2270 Approved
0.5918 Remote Similarity NPD9655 Approved
0.5893 Remote Similarity NPD9638 Phase 2
0.5882 Remote Similarity NPD5777 Approved
0.587 Remote Similarity NPD900 Approved
0.5862 Remote Similarity NPD3728 Approved
0.5862 Remote Similarity NPD3730 Approved
0.5849 Remote Similarity NPD9430 Approved
0.5849 Remote Similarity NPD9431 Approved
0.5821 Remote Similarity NPD3726 Approved
0.5821 Remote Similarity NPD3725 Approved
0.5781 Remote Similarity NPD7909 Approved
0.566 Remote Similarity NPD3199 Clinical (unspecified phase)
0.5634 Remote Similarity NPD3702 Approved
0.5616 Remote Similarity NPD4802 Phase 2
0.5616 Remote Similarity NPD4238 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