Structure

Physi-Chem Properties

Molecular Weight:  100.05
Volume:  107.344
LogP:  -0.488
LogD:  -1.711
LogS:  0.14
# Rotatable Bonds:  2
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.475
Synthetic Accessibility Score:  2.173
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.627
MDCK Permeability:  2.036796104221139e-05
Pgp-inhibitor:  0.012
Pgp-substrate:  0.54
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.744
Plasma Protein Binding (PPB):  30.50823211669922%
Volume Distribution (VD):  0.435
Pgp-substrate:  84.30713653564453%

ADMET: Metabolism

CYP1A2-inhibitor:  0.036
CYP1A2-substrate:  0.531
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.796
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.663
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.615
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.289

ADMET: Excretion

Clearance (CL):  7.603
Half-life (T1/2):  0.893

ADMET: Toxicity

hERG Blockers:  0.053
Human Hepatotoxicity (H-HT):  0.035
Drug-inuced Liver Injury (DILI):  0.387
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.702
Maximum Recommended Daily Dose:  0.396
Skin Sensitization:  0.912
Carcinogencity:  0.033
Eye Corrosion:  0.995
Eye Irritation:  0.982
Respiratory Toxicity:  0.971

Download Data

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

  Natural Product: NPC185768

Natural Product ID:  NPC185768
Common Name*:   Pentane-2,4-Dione
IUPAC Name:   pentane-2,4-dione
Synonyms:   Pentane-2,4-Dione
Standard InCHIKey:  YRKCREAYFQTBPV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H8O2/c1-4(6)3-5(2)7/h3H2,1-2H3
SMILES:  CC(=O)CC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL191625
PubChem CID:   31261
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000133] 1,3-dicarbonyl compounds
            • [CHEMONTID:0003926] Beta-diketones

*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
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota Flowers Tantempango, Hidalgo, Mexico 2019-May DOI[10.1007/s11130-020-00822-2]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota seeds Mengha, Yunnan Province, China 1991-Aug PMID[11277741]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota seeds n.a. n.a. PMID[11325233]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota Seeds n.a. n.a. PMID[11430002]
NPO3261 Aplysina archeri Species Aplysinidae Eukaryota n.a. n.a. n.a. PMID[1324982]
NPO6457 Pinus strobus Species Pinaceae Eukaryota n.a. heartwood n.a. PMID[13465274]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[1536925]
NPO14054 Penicillium janczewskii Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[16180822]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[16297615]
NPO422 Euphorbia cornigera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[17512094]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. whole plant n.a. PMID[18543151]
NPO422 Euphorbia cornigera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[19376614]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. seed n.a. PMID[24225786]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[24358188]
NPO2697 Monodora tenuifolia Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[3509958]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[8778246]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[9461664]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4564 Anguilla japonica Species Anguillidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24089 Alcea rosea Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2408 Millettia laurentii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4564 Anguilla japonica Species Anguillidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2997 Aloe africana Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24089 Alcea rosea Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2837 Aloe spicata Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7449 Eleutherobia albiflora Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3408 Viguiera decurrens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8058 Pluchea odorata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3956 Maesa ramentacea Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1489 Pseudoplexaura flagellosa Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7606 Salacia lehmbachii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1390 Melolontha melolontha Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7007 Eucalyptus jenseni Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25760 Aspergillus striatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5261 Sideroxylon cubense Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5584 Aldisa sanguinea Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2250 Hylocomium splendens Species Hylocomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6836 Alpinia blepharocalyx Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO295 Kokoona reflexa Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1242 Balanops australiana Species Balanopaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3261 Aplysina archeri Species Aplysinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO422 Euphorbia cornigera Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24089 Alcea rosea Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5975 Aspergillus carneus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO849 Euonymus tingens Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11747 Ocimum tenuiflorum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3554 Aonidiella aurantii Species Diaspididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18993 Araiostegiella perdurans Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2697 Monodora tenuifolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2408 Millettia laurentii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17593 Pinus sylvestris Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4564 Anguilla japonica Species Anguillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14054 Penicillium janczewskii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7760 Macrolepiota neomastoidea Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2997 Aloe africana Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15487 Gymnopus confluens Species Omphalotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2993 0totodarus sloanii Species Ommastrephidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6457 Pinus strobus Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4949 Salvia yosgadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3743 Sideritis brevibracteata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6231 Cortinarius odoratus Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4274 Alcyonium utinomii Species Alcyoniidae 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
NPT203 Individual Protein Carboxylesterase 2 Homo sapiens Ki > 100000.0 nM PMID[508852]
NPT166 Individual Protein Acyl coenzyme A:cholesterol acyltransferase Homo sapiens Ki > 100000.0 nM PMID[508852]
NPT2610 Individual Protein Acyl coenzyme A:cholesterol acyltransferase Oryctolagus cuniculus Ki > 100000.0 nM PMID[508852]
NPT204 Individual Protein Acetylcholinesterase Homo sapiens Ki > 100000.0 nM PMID[508852]
NPT439 Individual Protein Butyrylcholinesterase Homo sapiens Ki > 100000.0 nM PMID[508852]
NPT270 Individual Protein Nitric oxide synthase, inducible Mus musculus Inhibition = -6.0 % PMID[508853]
NPT150 Individual Protein Anthrax lethal factor Bacillus anthracis Inhibition = 5.0 % PMID[508853]
NPT280 Individual Protein Matrix metalloproteinase 9 Homo sapiens Inhibition = -17.0 % PMID[508853]
NPT569 Individual Protein Matrix metalloproteinase 8 Homo sapiens Inhibition = -6.0 % PMID[508853]
NPT570 Individual Protein Arachidonate 5-lipoxygenase Homo sapiens Inhibition = 42.0 % PMID[508853]
NPT567 Individual Protein Matrix metalloproteinase 3 Homo sapiens Inhibition = -4.0 % PMID[508853]
NPT568 Individual Protein Matrix metalloproteinase-2 Homo sapiens Inhibition = -5.0 % PMID[508853]
NPT43 Individual Protein Tyrosinase Agaricus bisporus Inhibition = 77.0 % PMID[508853]
NPT69 Individual Protein Matrix metalloproteinase-1 Homo sapiens Inhibition = 10.0 % PMID[508853]
NPT35 Others n.a. K = 3.8 /min PMID[508854]
NPT2 Others Unspecified Potency n.a. 57586.4 nM PubChem BioAssay data set

☑ 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 NPC185768 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
0.9524 High Similarity NPC222945
0.9091 High Similarity NPC33928
0.9048 High Similarity NPC141986
0.8696 High Similarity NPC30338
0.8636 High Similarity NPC32603
0.8571 High Similarity NPC147212
0.8095 Intermediate Similarity NPC211453
0.8095 Intermediate Similarity NPC171188
0.8 Intermediate Similarity NPC79591
0.76 Intermediate Similarity NPC66624
0.76 Intermediate Similarity NPC227197
0.76 Intermediate Similarity NPC307594
0.75 Intermediate Similarity NPC254524
0.72 Intermediate Similarity NPC91093
0.7083 Intermediate Similarity NPC83723
0.7037 Intermediate Similarity NPC100997
0.6923 Remote Similarity NPC129976
0.6897 Remote Similarity NPC302611
0.6897 Remote Similarity NPC168982
0.6786 Remote Similarity NPC295442
0.6667 Remote Similarity NPC200333
0.6667 Remote Similarity NPC228727
0.6562 Remote Similarity NPC121215
0.6552 Remote Similarity NPC42403
0.6552 Remote Similarity NPC221192
0.6552 Remote Similarity NPC4962
0.6552 Remote Similarity NPC248139
0.6552 Remote Similarity NPC29561
0.6552 Remote Similarity NPC79887
0.6552 Remote Similarity NPC196434
0.6552 Remote Similarity NPC153439
0.6552 Remote Similarity NPC222997
0.6538 Remote Similarity NPC164646
0.6452 Remote Similarity NPC94196
0.64 Remote Similarity NPC37479
0.6364 Remote Similarity NPC301919
0.6333 Remote Similarity NPC321646
0.6333 Remote Similarity NPC320981
0.6296 Remote Similarity NPC28246
0.625 Remote Similarity NPC127142
0.625 Remote Similarity NPC7814
0.625 Remote Similarity NPC248190
0.6207 Remote Similarity NPC38859
0.6207 Remote Similarity NPC198118
0.6154 Remote Similarity NPC203105
0.6154 Remote Similarity NPC8187
0.6129 Remote Similarity NPC225318
0.6129 Remote Similarity NPC268596
0.6129 Remote Similarity NPC76608
0.6129 Remote Similarity NPC16578
0.6129 Remote Similarity NPC149101
0.6071 Remote Similarity NPC59581
0.6071 Remote Similarity NPC149209
0.6 Remote Similarity NPC158107
0.6 Remote Similarity NPC174368
0.6 Remote Similarity NPC292641
0.6 Remote Similarity NPC270334
0.5862 Remote Similarity NPC143211
0.5806 Remote Similarity NPC5934
0.5758 Remote Similarity NPC307027
0.5714 Remote Similarity NPC109026
0.5714 Remote Similarity NPC41485
0.5714 Remote Similarity NPC289974
0.5714 Remote Similarity NPC317945
0.5714 Remote Similarity NPC304927
0.5714 Remote Similarity NPC32280
0.5667 Remote Similarity NPC55956
0.5667 Remote Similarity NPC32279
0.5667 Remote Similarity NPC287782
0.5625 Remote Similarity NPC280532
0.5625 Remote Similarity NPC12904
0.56 Remote Similarity NPC237869

  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 NPC185768 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
0.7037 Intermediate Similarity NPD106 Approved
0.6552 Remote Similarity NPD62 Approved
0.64 Remote Similarity NPD8616 Clinical (unspecified phase)
0.64 Remote Similarity NPD8615 Phase 2
0.6333 Remote Similarity NPD8590 Approved
0.625 Remote Similarity NPD8857 Approved
0.5862 Remote Similarity NPD8990 Clinical (unspecified phase)
0.5833 Remote Similarity NPD8200 Phase 2
0.5806 Remote Similarity NPD8856 Phase 2
0.5769 Remote Similarity NPD8190 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