Structure

Physi-Chem Properties

Molecular Weight:  156.12
Volume:  170.608
LogP:  2.87
LogD:  2.528
LogS:  -2.967
# Rotatable Bonds:  4
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.46
Synthetic Accessibility Score:  2.756
Fsp3:  0.889
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:  -4.435
MDCK Permeability:  3.506791472318582e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.869
30% Bioavailability (F30%):  0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.993
Plasma Protein Binding (PPB):  49.21460723876953%
Volume Distribution (VD):  0.974
Pgp-substrate:  60.02342224121094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.944
CYP1A2-substrate:  0.676
CYP2C19-inhibitor:  0.694
CYP2C19-substrate:  0.602
CYP2C9-inhibitor:  0.226
CYP2C9-substrate:  0.741
CYP2D6-inhibitor:  0.025
CYP2D6-substrate:  0.457
CYP3A4-inhibitor:  0.067
CYP3A4-substrate:  0.195

ADMET: Excretion

Clearance (CL):  9.556
Half-life (T1/2):  0.438

ADMET: Toxicity

hERG Blockers:  0.105
Human Hepatotoxicity (H-HT):  0.057
Drug-inuced Liver Injury (DILI):  0.05
AMES Toxicity:  0.022
Rat Oral Acute Toxicity:  0.04
Maximum Recommended Daily Dose:  0.05
Skin Sensitization:  0.877
Carcinogencity:  0.445
Eye Corrosion:  0.932
Eye Irritation:  0.984
Respiratory Toxicity:  0.394

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

  Natural Product: NPC305182

Natural Product ID:  NPC305182
Common Name*:   Gama-Nonalactone
IUPAC Name:   3-pentyloxolan-2-one
Synonyms:   Gama-Nonalactone
Standard InCHIKey:  ZWYZHNNHSZXTTG-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H16O2/c1-2-3-4-5-8-6-7-11-9(8)10/h8H,2-7H2,1H3
SMILES:  CCCCCC1CCOC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL476333
PubChem CID:   559675
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
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[12379786]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[23507362]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota Cotyledon n.a. n.a. Database[FooDB]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota Seed Oil n.a. n.a. Database[FooDB]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7530 Cucumis sativus Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7530 Cucumis sativus Species Cucurbitaceae 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 = 14.47 umol/min/mg PMID[495865]

☑ 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 NPC305182 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 NPC282440
0.8333 Intermediate Similarity NPC105329
0.8333 Intermediate Similarity NPC52700
0.8333 Intermediate Similarity NPC63182
0.8333 Intermediate Similarity NPC145045
0.8235 Intermediate Similarity NPC314084
0.8163 Intermediate Similarity NPC249754
0.8125 Intermediate Similarity NPC273545
0.807 Intermediate Similarity NPC306750
0.8043 Intermediate Similarity NPC256163
0.8043 Intermediate Similarity NPC250028
0.8043 Intermediate Similarity NPC149299
0.8043 Intermediate Similarity NPC40597
0.7959 Intermediate Similarity NPC314679
0.7959 Intermediate Similarity NPC308301
0.7872 Intermediate Similarity NPC53541
0.7826 Intermediate Similarity NPC223249
0.7826 Intermediate Similarity NPC80234
0.7778 Intermediate Similarity NPC319589
0.7755 Intermediate Similarity NPC55023
0.7708 Intermediate Similarity NPC176500
0.7708 Intermediate Similarity NPC203531
0.7708 Intermediate Similarity NPC236579
0.7667 Intermediate Similarity NPC157518
0.766 Intermediate Similarity NPC165533
0.7647 Intermediate Similarity NPC13105
0.7647 Intermediate Similarity NPC477878
0.7647 Intermediate Similarity NPC324793
0.7609 Intermediate Similarity NPC305660
0.7609 Intermediate Similarity NPC201622
0.7609 Intermediate Similarity NPC54980
0.7609 Intermediate Similarity NPC22903
0.7609 Intermediate Similarity NPC316546
0.7586 Intermediate Similarity NPC478126
0.7451 Intermediate Similarity NPC21844
0.7447 Intermediate Similarity NPC31551
0.7447 Intermediate Similarity NPC81263
0.7447 Intermediate Similarity NPC219536
0.74 Intermediate Similarity NPC287231
0.74 Intermediate Similarity NPC47363
0.7391 Intermediate Similarity NPC14608
0.7377 Intermediate Similarity NPC469926
0.7302 Intermediate Similarity NPC82315
0.7292 Intermediate Similarity NPC28598
0.7292 Intermediate Similarity NPC12156
0.7292 Intermediate Similarity NPC161097
0.7273 Intermediate Similarity NPC72722
0.7213 Intermediate Similarity NPC314103
0.72 Intermediate Similarity NPC317128
0.7188 Intermediate Similarity NPC5714
0.7188 Intermediate Similarity NPC296522
0.7188 Intermediate Similarity NPC295788
0.7188 Intermediate Similarity NPC199557
0.7188 Intermediate Similarity NPC144511
0.7174 Intermediate Similarity NPC80641
0.7174 Intermediate Similarity NPC80396
0.7174 Intermediate Similarity NPC154642
0.7143 Intermediate Similarity NPC248763
0.7143 Intermediate Similarity NPC325452
0.7143 Intermediate Similarity NPC469925
0.7119 Intermediate Similarity NPC470363
0.7119 Intermediate Similarity NPC472020
0.7119 Intermediate Similarity NPC472019
0.7119 Intermediate Similarity NPC226602
0.7115 Intermediate Similarity NPC326957
0.7083 Intermediate Similarity NPC94368
0.7077 Intermediate Similarity NPC472955
0.7037 Intermediate Similarity NPC142103
0.7 Intermediate Similarity NPC472021
0.6984 Remote Similarity NPC135043
0.6984 Remote Similarity NPC315525
0.6984 Remote Similarity NPC84562
0.697 Remote Similarity NPC470243
0.6957 Remote Similarity NPC223374
0.6957 Remote Similarity NPC155872
0.6957 Remote Similarity NPC86545
0.6957 Remote Similarity NPC301398
0.6957 Remote Similarity NPC196442
0.6957 Remote Similarity NPC156630
0.6923 Remote Similarity NPC28526
0.6923 Remote Similarity NPC12438
0.6923 Remote Similarity NPC30195
0.6909 Remote Similarity NPC274261
0.6909 Remote Similarity NPC291724
0.6885 Remote Similarity NPC469922
0.6875 Remote Similarity NPC469868
0.6866 Remote Similarity NPC475232
0.6866 Remote Similarity NPC109510
0.6866 Remote Similarity NPC474100
0.6866 Remote Similarity NPC475260
0.6866 Remote Similarity NPC473699
0.6866 Remote Similarity NPC51249
0.6866 Remote Similarity NPC473775
0.6866 Remote Similarity NPC474755
0.6852 Remote Similarity NPC26253
0.6833 Remote Similarity NPC475821
0.6825 Remote Similarity NPC295256
0.6825 Remote Similarity NPC215987
0.6825 Remote Similarity NPC306805
0.6774 Remote Similarity NPC235788
0.6769 Remote Similarity NPC119838
0.6765 Remote Similarity NPC469641
0.6765 Remote Similarity NPC55508
0.6765 Remote Similarity NPC472966
0.6765 Remote Similarity NPC469643
0.6765 Remote Similarity NPC215030
0.6739 Remote Similarity NPC286498
0.6739 Remote Similarity NPC154396
0.6735 Remote Similarity NPC14227
0.6735 Remote Similarity NPC261080
0.6735 Remote Similarity NPC201844
0.6735 Remote Similarity NPC301585
0.6735 Remote Similarity NPC113928
0.6735 Remote Similarity NPC301696
0.6735 Remote Similarity NPC154186
0.6735 Remote Similarity NPC3531
0.6735 Remote Similarity NPC279026
0.6727 Remote Similarity NPC55678
0.6716 Remote Similarity NPC129665
0.6667 Remote Similarity NPC98711
0.6667 Remote Similarity NPC179922
0.6667 Remote Similarity NPC155587
0.6667 Remote Similarity NPC471491
0.6667 Remote Similarity NPC138408
0.6667 Remote Similarity NPC106872
0.6667 Remote Similarity NPC128996
0.6667 Remote Similarity NPC324762
0.6667 Remote Similarity NPC193351
0.6667 Remote Similarity NPC69245
0.6667 Remote Similarity NPC226669
0.6667 Remote Similarity NPC228411
0.6618 Remote Similarity NPC472956
0.6615 Remote Similarity NPC286842
0.6613 Remote Similarity NPC253204
0.6607 Remote Similarity NPC287811
0.6571 Remote Similarity NPC41017
0.6571 Remote Similarity NPC266159
0.6571 Remote Similarity NPC472959
0.6571 Remote Similarity NPC476601
0.6571 Remote Similarity NPC472967
0.6571 Remote Similarity NPC235906
0.6571 Remote Similarity NPC92489
0.6562 Remote Similarity NPC476330
0.6557 Remote Similarity NPC469924
0.6545 Remote Similarity NPC250919
0.6531 Remote Similarity NPC223315
0.6522 Remote Similarity NPC477867
0.6522 Remote Similarity NPC286695
0.6522 Remote Similarity NPC35371
0.6522 Remote Similarity NPC41007
0.6522 Remote Similarity NPC320537
0.6522 Remote Similarity NPC178643
0.6522 Remote Similarity NPC143979
0.6522 Remote Similarity NPC322892
0.6522 Remote Similarity NPC168714
0.6515 Remote Similarity NPC319007
0.6508 Remote Similarity NPC474552
0.6491 Remote Similarity NPC310746
0.6481 Remote Similarity NPC328497
0.6481 Remote Similarity NPC324004
0.6479 Remote Similarity NPC15975
0.6479 Remote Similarity NPC65603
0.6479 Remote Similarity NPC143250
0.6479 Remote Similarity NPC41780
0.6479 Remote Similarity NPC476794
0.6479 Remote Similarity NPC470240
0.6479 Remote Similarity NPC187568
0.6479 Remote Similarity NPC195785
0.6479 Remote Similarity NPC307865
0.6471 Remote Similarity NPC307783
0.6471 Remote Similarity NPC209970
0.6471 Remote Similarity NPC149184
0.6471 Remote Similarity NPC171736
0.6471 Remote Similarity NPC163003
0.6471 Remote Similarity NPC469940
0.6471 Remote Similarity NPC216630
0.6471 Remote Similarity NPC197701
0.6471 Remote Similarity NPC196924
0.6458 Remote Similarity NPC321699
0.6452 Remote Similarity NPC66145
0.6452 Remote Similarity NPC469921
0.6429 Remote Similarity NPC217725
0.6429 Remote Similarity NPC81052
0.6418 Remote Similarity NPC178541
0.6418 Remote Similarity NPC475062
0.64 Remote Similarity NPC183424
0.64 Remote Similarity NPC118968
0.64 Remote Similarity NPC214610
0.64 Remote Similarity NPC294085
0.6389 Remote Similarity NPC475616
0.6389 Remote Similarity NPC11796
0.6389 Remote Similarity NPC470014
0.6389 Remote Similarity NPC218817
0.6389 Remote Similarity NPC35574
0.6383 Remote Similarity NPC57499
0.6377 Remote Similarity NPC295633
0.6377 Remote Similarity NPC475230
0.6377 Remote Similarity NPC248567
0.6377 Remote Similarity NPC269206
0.6377 Remote Similarity NPC58956

  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 NPC305182 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
0.7959 Intermediate Similarity NPD634 Phase 3
0.7708 Intermediate Similarity NPD387 Clinical (unspecified phase)
0.74 Intermediate Similarity NPD2699 Approved
0.7391 Intermediate Similarity NPD9449 Clinical (unspecified phase)
0.7143 Intermediate Similarity NPD615 Clinical (unspecified phase)
0.7119 Intermediate Similarity NPD3198 Approved
0.7091 Intermediate Similarity NPD3186 Phase 1
0.6957 Remote Similarity NPD9447 Approved
0.6875 Remote Similarity NPD3206 Approved
0.6842 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6825 Remote Similarity NPD9496 Clinical (unspecified phase)
0.6769 Remote Similarity NPD229 Approved
0.6735 Remote Similarity NPD77 Approved
0.6735 Remote Similarity NPD9450 Approved
0.6735 Remote Similarity NPD9448 Phase 2
0.6735 Remote Similarity NPD633 Phase 3
0.6667 Remote Similarity NPD2266 Phase 2
0.6667 Remote Similarity NPD6125 Clinical (unspecified phase)
0.6471 Remote Similarity NPD2270 Approved
0.6471 Remote Similarity NPD5777 Approved
0.6418 Remote Similarity NPD3725 Approved
0.6418 Remote Similarity NPD3726 Approved
0.6406 Remote Similarity NPD7909 Approved
0.64 Remote Similarity NPD9655 Approved
0.6271 Remote Similarity NPD3730 Approved
0.6271 Remote Similarity NPD3728 Approved
0.623 Remote Similarity NPD4279 Approved
0.6197 Remote Similarity NPD3702 Approved
0.6164 Remote Similarity NPD4802 Phase 2
0.6164 Remote Similarity NPD4238 Approved
0.6111 Remote Similarity NPD3199 Clinical (unspecified phase)
0.6034 Remote Similarity NPD9638 Phase 2
0.6032 Remote Similarity NPD4280 Approved
0.6 Remote Similarity NPD9430 Approved
0.6 Remote Similarity NPD9431 Approved
0.5972 Remote Similarity NPD2257 Approved
0.597 Remote Similarity NPD4224 Phase 2
0.5962 Remote Similarity NPD1460 Approved
0.5962 Remote Similarity NPD9635 Discontinued
0.5942 Remote Similarity NPD2697 Approved
0.5942 Remote Similarity NPD2696 Approved
0.5942 Remote Similarity NPD2695 Approved
0.5942 Remote Similarity NPD2694 Approved
0.5846 Remote Similarity NPD9676 Phase 3
0.5833 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5823 Remote Similarity NPD1694 Approved
0.5823 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5821 Remote Similarity NPD3171 Clinical (unspecified phase)
0.5753 Remote Similarity NPD8039 Approved
0.5741 Remote Similarity NPD1462 Approved
0.5735 Remote Similarity NPD375 Phase 2
0.5714 Remote Similarity NPD1780 Approved
0.5714 Remote Similarity NPD900 Approved
0.5714 Remote Similarity NPD1779 Approved
0.5714 Remote Similarity NPD5369 Approved
0.5692 Remote Similarity NPD9656 Approved
0.5676 Remote Similarity NPD6117 Approved
0.5641 Remote Similarity NPD6435 Approved
0.5641 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5614 Remote Similarity NPD343 Approved
0.5614 Remote Similarity NPD344 Approved
0.5614 Remote Similarity NPD345 Approved
0.56 Remote Similarity NPD6116 Phase 1

  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