Structure

Physi-Chem Properties

Molecular Weight:  86.04
Volume:  84.128
LogP:  0.723
LogD:  0.702
LogS:  -0.501
# Rotatable Bonds:  0
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.397
Synthetic Accessibility Score:  2.674
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.462
MDCK Permeability:  0.00010642025154083967
Pgp-inhibitor:  0.005
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.791

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.984
Plasma Protein Binding (PPB):  9.602153778076172%
Volume Distribution (VD):  0.732
Pgp-substrate:  82.58086395263672%

ADMET: Metabolism

CYP1A2-inhibitor:  0.293
CYP1A2-substrate:  0.095
CYP2C19-inhibitor:  0.036
CYP2C19-substrate:  0.451
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.115
CYP2D6-inhibitor:  0.018
CYP2D6-substrate:  0.373
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.239

ADMET: Excretion

Clearance (CL):  11.172
Half-life (T1/2):  0.817

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.263
Drug-inuced Liver Injury (DILI):  0.439
AMES Toxicity:  0.962
Rat Oral Acute Toxicity:  0.137
Maximum Recommended Daily Dose:  0.142
Skin Sensitization:  0.706
Carcinogencity:  0.912
Eye Corrosion:  0.996
Eye Irritation:  0.993
Respiratory Toxicity:  0.178

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

  Natural Product: NPC217218

Natural Product ID:  NPC217218
Common Name*:   Beta-Hydroxybutrolactone
IUPAC Name:   (4S)-4-methyloxetan-2-one
Synonyms:   Beta-Hydroxybutrolactone
Standard InCHIKey:  GSCLMSFRWBPUSK-VKHMYHEASA-N
Standard InCHI:  InChI=1S/C4H6O2/c1-3-2-4(5)6-3/h3H,2H2,1H3/t3-/m0/s1
SMILES:  C[C@H]1CC(=O)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL452927
PubChem CID:   6998969
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001243] Beta propiolactones

*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
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[11374978]
NPO17823 Lycium chinense Species Solanaceae Eukaryota fruits n.a. n.a. PMID[12467621]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[12932131]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15679317]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. root n.a. PMID[16212233]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[17997069]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[20460582]
NPO17823 Lycium chinense Species Solanaceae Eukaryota root bark n.a. n.a. PMID[23282106]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[25172746]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO17823 Lycium chinense Species Solanaceae Eukaryota Root Bark n.a. n.a. PMID[26982999]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[31397570]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8910532]
NPO17823 Lycium chinense Species Solanaceae Eukaryota fruits n.a. n.a. PMID[9090870]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11438 Angelica gigas Species Apiaceae 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 = 3.83 umol/min/mg PMID[564987]

☑ 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 NPC217218 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
0.7742 Intermediate Similarity NPC143211
0.7576 Intermediate Similarity NPC302611
0.7419 Intermediate Similarity NPC166804
0.7419 Intermediate Similarity NPC127134
0.7222 Intermediate Similarity NPC250870
0.7222 Intermediate Similarity NPC168052
0.7222 Intermediate Similarity NPC191084
0.7097 Intermediate Similarity NPC41485
0.7097 Intermediate Similarity NPC3693
0.7097 Intermediate Similarity NPC28246
0.7097 Intermediate Similarity NPC32280
0.7059 Intermediate Similarity NPC265882
0.7059 Intermediate Similarity NPC21374
0.7027 Intermediate Similarity NPC321699
0.697 Remote Similarity NPC234005
0.697 Remote Similarity NPC88135
0.6857 Remote Similarity NPC12904
0.6774 Remote Similarity NPC110107
0.6667 Remote Similarity NPC168714
0.6667 Remote Similarity NPC108238
0.6667 Remote Similarity NPC41007
0.6667 Remote Similarity NPC248233
0.6667 Remote Similarity NPC286695
0.6667 Remote Similarity NPC178643
0.6667 Remote Similarity NPC35371
0.6571 Remote Similarity NPC320981
0.6571 Remote Similarity NPC5934
0.65 Remote Similarity NPC94368
0.6486 Remote Similarity NPC154396
0.6471 Remote Similarity NPC317739
0.6471 Remote Similarity NPC55956
0.6471 Remote Similarity NPC281943
0.6452 Remote Similarity NPC8187
0.6452 Remote Similarity NPC203105
0.6452 Remote Similarity NPC23508
0.6389 Remote Similarity NPC281883
0.6364 Remote Similarity NPC201132
0.6286 Remote Similarity NPC180423
0.6286 Remote Similarity NPC127696
0.6216 Remote Similarity NPC99700
0.6216 Remote Similarity NPC322892
0.6176 Remote Similarity NPC283626
0.6154 Remote Similarity NPC80396
0.6154 Remote Similarity NPC233231
0.6154 Remote Similarity NPC5505
0.6154 Remote Similarity NPC103612
0.6154 Remote Similarity NPC24967
0.6154 Remote Similarity NPC154642
0.6154 Remote Similarity NPC80641
0.6061 Remote Similarity NPC35155
0.6047 Remote Similarity NPC176500
0.6 Remote Similarity NPC37493
0.6 Remote Similarity NPC133771
0.6 Remote Similarity NPC14608
0.5946 Remote Similarity NPC228727
0.5946 Remote Similarity NPC40965
0.5897 Remote Similarity NPC289344
0.5897 Remote Similarity NPC325165
0.5897 Remote Similarity NPC155872
0.5882 Remote Similarity NPC211250
0.5882 Remote Similarity NPC149209
0.5833 Remote Similarity NPC248139
0.5833 Remote Similarity NPC292641
0.5814 Remote Similarity NPC97444
0.5814 Remote Similarity NPC100742
0.5814 Remote Similarity NPC121018
0.5814 Remote Similarity NPC192402
0.5814 Remote Similarity NPC35661
0.5814 Remote Similarity NPC19044
0.5814 Remote Similarity NPC24751
0.5778 Remote Similarity NPC287231
0.5778 Remote Similarity NPC47363
0.5778 Remote Similarity NPC273545
0.5758 Remote Similarity NPC8368
0.5714 Remote Similarity NPC222792
0.5714 Remote Similarity NPC81263
0.5714 Remote Similarity NPC80234
0.5714 Remote Similarity NPC316217
0.5682 Remote Similarity NPC325102
0.5676 Remote Similarity NPC198126
0.5667 Remote Similarity NPC137050
0.5652 Remote Similarity NPC145045
0.5652 Remote Similarity NPC105329
0.5652 Remote Similarity NPC63182
0.5652 Remote Similarity NPC52700
0.5641 Remote Similarity NPC286498
0.5641 Remote Similarity NPC57499
0.5641 Remote Similarity NPC140229
0.5625 Remote Similarity NPC46254
0.56 Remote Similarity NPC35816
0.56 Remote Similarity NPC325180

  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 NPC217218 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
0.7667 Intermediate Similarity NPD8188 Approved
0.7419 Intermediate Similarity NPD8989 Approved
0.7188 Intermediate Similarity NPD106 Approved
0.6667 Remote Similarity NPD8616 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8615 Phase 2
0.6571 Remote Similarity NPD8590 Approved
0.6571 Remote Similarity NPD8856 Phase 2
0.6486 Remote Similarity NPD900 Approved
0.6389 Remote Similarity NPD9636 Phase 2
0.5833 Remote Similarity NPD8619 Approved
0.5833 Remote Similarity NPD62 Approved
0.5833 Remote Similarity NPD8617 Approved
0.5814 Remote Similarity NPD8604 Approved
0.5814 Remote Similarity NPD8599 Approved
0.5814 Remote Similarity NPD8603 Approved
0.5814 Remote Similarity NPD8605 Approved
0.5814 Remote Similarity NPD8602 Approved
0.5814 Remote Similarity NPD8601 Approved
0.5814 Remote Similarity NPD8600 Approved
0.5814 Remote Similarity NPD8598 Approved
0.5778 Remote Similarity NPD2699 Approved
0.5714 Remote Similarity NPD8990 Clinical (unspecified phase)
0.5676 Remote Similarity NPD8618 Approved
0.5676 Remote Similarity NPD54 Approved
0.5676 Remote Similarity NPD55 Approved
0.5676 Remote Similarity NPD8206 Approved
0.5676 Remote Similarity NPD8204 Approved
0.5676 Remote Similarity NPD8203 Approved
0.5667 Remote Similarity NPD8200 Phase 2
0.561 Remote Similarity NPD9131 Discovery
0.56 Remote Similarity NPD9660 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