Structure

Physi-Chem Properties

Molecular Weight:  130.06
Volume:  127.51
LogP:  -0.016
LogD:  0.409
LogS:  -0.988
# Rotatable Bonds:  0
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.472
Synthetic Accessibility Score:  3.525
Fsp3:  0.833
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:  -4.575
MDCK Permeability:  6.149277032818645e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.061

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.871
Plasma Protein Binding (PPB):  12.100950241088867%
Volume Distribution (VD):  0.671
Pgp-substrate:  81.89305114746094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.108
CYP1A2-substrate:  0.543
CYP2C19-inhibitor:  0.099
CYP2C19-substrate:  0.764
CYP2C9-inhibitor:  0.014
CYP2C9-substrate:  0.244
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.137
CYP3A4-inhibitor:  0.024
CYP3A4-substrate:  0.257

ADMET: Excretion

Clearance (CL):  7.289
Half-life (T1/2):  0.797

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.033
Drug-inuced Liver Injury (DILI):  0.127
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.009
Maximum Recommended Daily Dose:  0.06
Skin Sensitization:  0.444
Carcinogencity:  0.064
Eye Corrosion:  0.961
Eye Irritation:  0.978
Respiratory Toxicity:  0.029

Download Data

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

  Natural Product: NPC133771

Natural Product ID:  NPC133771
Common Name*:   (4R)-4-Hydroxy-4-Methyloxan-2-One
IUPAC Name:   (4R)-4-hydroxy-4-methyloxan-2-one
Synonyms:  
Standard InCHIKey:  JYVXNLLUYHCIIH-ZCFIWIBFSA-N
Standard InCHI:  InChI=1S/C6H10O3/c1-6(8)2-3-9-5(7)4-6/h8H,2-4H2,1H3/t6-/m1/s1
SMILES:  C[C@]1(CCOC(=O)C1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1401520
PubChem CID:   6419891
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001244] Delta valerolactones

*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
NPO28230 Stemona japonica Species Stemonaceae Eukaryota stems and leaves n.a. n.a. PMID[18163592]
NPO16660 Phomopsis archeri Species Valsaceae Eukaryota n.a. mycelium n.a. PMID[21341709]
NPO28178 Artemisia tridentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28560 Sarcomelicope glauca Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28407 Clausena heptaphylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28560 Sarcomelicope glauca Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28407 Clausena heptaphylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28178 Artemisia tridentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28407 Clausena heptaphylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27851 Leptothorax muscorum Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28108 Stereum princeps Species Stereaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28350 Hypsizigus marmoreus n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16660 Phomopsis archeri Species Valsaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28407 Clausena heptaphylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23206 Senegalia caffra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29474 Bipolaris victoriae Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28178 Artemisia tridentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28463 Penicillium gilmanii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28560 Sarcomelicope glauca Species Rutaceae 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
NPT483 Individual Protein Prelamin-A/C Homo sapiens Potency = 14125.4 nM PMID[551718]
NPT212 Individual Protein Cytochrome P450 2C9 Homo sapiens Potency = 12589.3 nM PMID[551718]
NPT444 Individual Protein Ubiquitin carboxyl-terminal hydrolase 1 Homo sapiens Potency n.a. 39810.7 nM PMID[551718]

☑ 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 NPC133771 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
0.8 Intermediate Similarity NPC310220
0.7407 Intermediate Similarity NPC198377
0.7308 Intermediate Similarity NPC317680
0.717 Intermediate Similarity NPC65985
0.7143 Intermediate Similarity NPC99700
0.7143 Intermediate Similarity NPC179624
0.7018 Intermediate Similarity NPC469924
0.6909 Remote Similarity NPC68743
0.6909 Remote Similarity NPC60830
0.6818 Remote Similarity NPC168052
0.6818 Remote Similarity NPC250870
0.6818 Remote Similarity NPC191084
0.6731 Remote Similarity NPC293378
0.6731 Remote Similarity NPC46254
0.6727 Remote Similarity NPC6883
0.6724 Remote Similarity NPC475821
0.6667 Remote Similarity NPC61567
0.6545 Remote Similarity NPC19676
0.6545 Remote Similarity NPC323401
0.6522 Remote Similarity NPC206924
0.6512 Remote Similarity NPC280532
0.6429 Remote Similarity NPC174368
0.64 Remote Similarity NPC319680
0.6393 Remote Similarity NPC474552
0.6393 Remote Similarity NPC235788
0.6383 Remote Similarity NPC38930
0.6383 Remote Similarity NPC325454
0.6379 Remote Similarity NPC220922
0.6364 Remote Similarity NPC94196
0.6364 Remote Similarity NPC286695
0.6304 Remote Similarity NPC321699
0.6279 Remote Similarity NPC21374
0.625 Remote Similarity NPC3531
0.623 Remote Similarity NPC469923
0.6226 Remote Similarity NPC200618
0.6226 Remote Similarity NPC131770
0.6222 Remote Similarity NPC127142
0.6222 Remote Similarity NPC7814
0.617 Remote Similarity NPC252843
0.617 Remote Similarity NPC14608
0.6167 Remote Similarity NPC472020
0.6167 Remote Similarity NPC472019
0.6167 Remote Similarity NPC226602
0.6136 Remote Similarity NPC12904
0.6136 Remote Similarity NPC228727
0.6122 Remote Similarity NPC240109
0.6087 Remote Similarity NPC316685
0.6087 Remote Similarity NPC317203
0.6066 Remote Similarity NPC472021
0.6061 Remote Similarity NPC98711
0.6047 Remote Similarity NPC61066
0.6047 Remote Similarity NPC104195
0.6047 Remote Similarity NPC122768
0.6047 Remote Similarity NPC151140
0.6038 Remote Similarity NPC326957
0.6 Remote Similarity NPC125575
0.6 Remote Similarity NPC41007
0.6 Remote Similarity NPC248763
0.6 Remote Similarity NPC469925
0.6 Remote Similarity NPC90904
0.6 Remote Similarity NPC325452
0.6 Remote Similarity NPC35371
0.6 Remote Similarity NPC175342
0.6 Remote Similarity NPC178643
0.6 Remote Similarity NPC217218
0.6 Remote Similarity NPC168714
0.5968 Remote Similarity NPC10659
0.5957 Remote Similarity NPC80396
0.5957 Remote Similarity NPC154642
0.5952 Remote Similarity NPC248233
0.5952 Remote Similarity NPC143211
0.5942 Remote Similarity NPC477867
0.5938 Remote Similarity NPC469926
0.5938 Remote Similarity NPC476330
0.5918 Remote Similarity NPC81263
0.5918 Remote Similarity NPC222792
0.5918 Remote Similarity NPC94368
0.5918 Remote Similarity NPC316217
0.5915 Remote Similarity NPC474003
0.5909 Remote Similarity NPC302611
0.5909 Remote Similarity NPC320981
0.5909 Remote Similarity NPC265882
0.5882 Remote Similarity NPC325102
0.5873 Remote Similarity NPC317651
0.5873 Remote Similarity NPC258690
0.587 Remote Similarity NPC307027
0.587 Remote Similarity NPC154396
0.5849 Remote Similarity NPC282440
0.5849 Remote Similarity NPC308301
0.5833 Remote Similarity NPC293692
0.5833 Remote Similarity NPC109026
0.5814 Remote Similarity NPC317739
0.5814 Remote Similarity NPC281943
0.5806 Remote Similarity NPC469921
0.5789 Remote Similarity NPC277878
0.5781 Remote Similarity NPC314103
0.5778 Remote Similarity NPC328569
0.5745 Remote Similarity NPC155872
0.5745 Remote Similarity NPC289344
0.5738 Remote Similarity NPC320032
0.5714 Remote Similarity NPC166804
0.5714 Remote Similarity NPC316546
0.5714 Remote Similarity NPC263732
0.5714 Remote Similarity NPC149209
0.5692 Remote Similarity NPC215987
0.5692 Remote Similarity NPC306805
0.569 Remote Similarity NPC196612
0.5686 Remote Similarity NPC35661
0.566 Remote Similarity NPC270088
0.566 Remote Similarity NPC242655
0.566 Remote Similarity NPC38891
0.5652 Remote Similarity NPC18224
0.5652 Remote Similarity NPC96322
0.5652 Remote Similarity NPC322892
0.5652 Remote Similarity NPC478227
0.5652 Remote Similarity NPC320119
0.5652 Remote Similarity NPC328710
0.5645 Remote Similarity NPC17935
0.5645 Remote Similarity NPC470363
0.5636 Remote Similarity NPC106872
0.5625 Remote Similarity NPC5505
0.5625 Remote Similarity NPC155263
0.5625 Remote Similarity NPC80641
0.5616 Remote Similarity NPC127526
0.56 Remote Similarity NPC80234

  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 NPC133771 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
0.6731 Remote Similarity NPD9126 Approved
0.6731 Remote Similarity NPD71 Approved
0.6731 Remote Similarity NPD9129 Approved
0.6538 Remote Similarity NPD109 Approved
0.6538 Remote Similarity NPD9130 Phase 3
0.6538 Remote Similarity NPD9124 Approved
0.6538 Remote Similarity NPD9127 Approved
0.6538 Remote Similarity NPD70 Approved
0.6538 Remote Similarity NPD108 Approved
0.6538 Remote Similarity NPD9121 Approved
0.6538 Remote Similarity NPD9125 Approved
0.6538 Remote Similarity NPD9128 Approved
0.6538 Remote Similarity NPD9123 Approved
0.6538 Remote Similarity NPD9122 Approved
0.6379 Remote Similarity NPD8959 Approved
0.6327 Remote Similarity NPD9116 Phase 1
0.625 Remote Similarity NPD9450 Approved
0.625 Remote Similarity NPD77 Approved
0.6226 Remote Similarity NPD2266 Phase 2
0.6222 Remote Similarity NPD8857 Approved
0.6122 Remote Similarity NPD9635 Discontinued
0.5909 Remote Similarity NPD8590 Approved
0.5873 Remote Similarity NPD8961 Approved
0.5789 Remote Similarity NPD72 Approved
0.5789 Remote Similarity NPD66 Approved
0.5789 Remote Similarity NPD8960 Approved
0.5789 Remote Similarity NPD9008 Approved
0.5789 Remote Similarity NPD9011 Approved
0.5789 Remote Similarity NPD9010 Approved
0.5789 Remote Similarity NPD9009 Approved
0.5789 Remote Similarity NPD9007 Approved
0.5789 Remote Similarity NPD65 Approved
0.5789 Remote Similarity NPD64 Approved
0.5745 Remote Similarity NPD9447 Approved
0.5714 Remote Similarity NPD9212 Clinical (unspecified phase)
0.5614 Remote Similarity NPD9638 Phase 2

  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