Structure

Physi-Chem Properties

Molecular Weight:  130.03
Volume:  122.288
LogP:  -0.769
LogD:  -1.447
LogS:  -0.033
# Rotatable Bonds:  3
TPSA:  71.44
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.417
Synthetic Accessibility Score:  2.444
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.492
MDCK Permeability:  0.00010683843720471486
Pgp-inhibitor:  0.004
Pgp-substrate:  0.044
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.083
Plasma Protein Binding (PPB):  27.255252838134766%
Volume Distribution (VD):  0.264
Pgp-substrate:  68.5162353515625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.014
CYP1A2-substrate:  0.079
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.03
CYP2C9-substrate:  0.757
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.157
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.113

ADMET: Excretion

Clearance (CL):  4.307
Half-life (T1/2):  0.9

ADMET: Toxicity

hERG Blockers:  0.048
Human Hepatotoxicity (H-HT):  0.059
Drug-inuced Liver Injury (DILI):  0.761
AMES Toxicity:  0.023
Rat Oral Acute Toxicity:  0.064
Maximum Recommended Daily Dose:  0.006
Skin Sensitization:  0.864
Carcinogencity:  0.015
Eye Corrosion:  0.997
Eye Irritation:  0.986
Respiratory Toxicity:  0.952

Download Data

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

  Natural Product: NPC317945

Natural Product ID:  NPC317945
Common Name*:   2,4-Dioxopentanoic Acid
IUPAC Name:   2,4-dioxopentanoic acid
Synonyms:   2,4-Dioxo-Pentanoic Acid; 2,4-Dioxopentanoic Acid; Acetopyruvate2,4-Dioxo-Pentanoic Acid
Standard InCHIKey:  UNRQTHVKJQUDDF-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H6O4/c1-3(6)2-4(7)5(8)9/h2H2,1H3,(H,8,9)
SMILES:  CC(=O)CC(=O)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL46789
PubChem CID:   21919
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000389] Keto acids and derivatives
        • [CHEMONTID:0001115] Gamma-keto acids and derivatives
          • [CHEMONTID:0004268] 3-Acylpyruvic acids

*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
NPO23622 Pseudomonas putida Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[1254564]
NPO23622 Pseudomonas putida Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[26195800]
NPO23622 Pseudomonas putida Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[8626242]
NPO23622 Pseudomonas putida Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[MetaboLights]
NPO23622 Pseudomonas putida Species Pseudomonadaceae Bacteria 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
NPT1758 Individual Protein Hepatitis C virus NS5B RNA-dependent RNA polymerase Hepatitis C virus IC50 > 50000.0 nM PMID[523545]
NPT27 Others Unspecified Binding energy = 9.1 kCal mol-1 PMID[523544]
NPT191 Organism Hepatitis C virus Hepatitis C virus IC50 = 50000.0 nM PMID[523546]

☑ 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 NPC317945 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
0.8649 High Similarity NPC128713
0.8571 High Similarity NPC7814
0.8571 High Similarity NPC127142
0.8108 Intermediate Similarity NPC1037
0.7941 Intermediate Similarity NPC292641
0.7941 Intermediate Similarity NPC248139
0.7895 Intermediate Similarity NPC109026
0.7805 Intermediate Similarity NPC289686
0.7692 Intermediate Similarity NPC38930
0.7429 Intermediate Similarity NPC174368
0.7222 Intermediate Similarity NPC320981
0.7143 Intermediate Similarity NPC236709
0.7105 Intermediate Similarity NPC307027
0.7059 Intermediate Similarity NPC286233
0.6842 Remote Similarity NPC125575
0.6842 Remote Similarity NPC175342
0.6842 Remote Similarity NPC18224
0.6842 Remote Similarity NPC328710
0.6667 Remote Similarity NPC242655
0.6667 Remote Similarity NPC38891
0.6585 Remote Similarity NPC206924
0.6571 Remote Similarity NPC149209
0.6512 Remote Similarity NPC320331
0.6512 Remote Similarity NPC240109
0.6458 Remote Similarity NPC293378
0.6444 Remote Similarity NPC319680
0.6429 Remote Similarity NPC325454
0.6364 Remote Similarity NPC121018
0.6364 Remote Similarity NPC24751
0.6364 Remote Similarity NPC100742
0.6364 Remote Similarity NPC192402
0.6364 Remote Similarity NPC97444
0.6364 Remote Similarity NPC19044
0.6341 Remote Similarity NPC134782
0.6341 Remote Similarity NPC155263
0.6341 Remote Similarity NPC5505
0.6279 Remote Similarity NPC329545
0.6275 Remote Similarity NPC65985
0.6222 Remote Similarity NPC310220
0.619 Remote Similarity NPC252843
0.619 Remote Similarity NPC158179
0.6154 Remote Similarity NPC212144
0.6154 Remote Similarity NPC280532
0.6098 Remote Similarity NPC317203
0.6087 Remote Similarity NPC74845
0.6053 Remote Similarity NPC61066
0.6053 Remote Similarity NPC151140
0.6053 Remote Similarity NPC122768
0.6053 Remote Similarity NPC104195
0.6053 Remote Similarity NPC180423
0.6047 Remote Similarity NPC73245
0.6047 Remote Similarity NPC268826
0.6042 Remote Similarity NPC101249
0.6038 Remote Similarity NPC60830
0.6038 Remote Similarity NPC68743
0.6 Remote Similarity NPC35661
0.5962 Remote Similarity NPC19676
0.5962 Remote Similarity NPC323401
0.5952 Remote Similarity NPC321699
0.5926 Remote Similarity NPC198377
0.5909 Remote Similarity NPC154186
0.5909 Remote Similarity NPC294085
0.5909 Remote Similarity NPC316217
0.5909 Remote Similarity NPC3531
0.5909 Remote Similarity NPC183424
0.5909 Remote Similarity NPC113928
0.5909 Remote Similarity NPC14227
0.5909 Remote Similarity NPC222792
0.5909 Remote Similarity NPC214610
0.5909 Remote Similarity NPC118968
0.5909 Remote Similarity NPC301585
0.5909 Remote Similarity NPC301696
0.5909 Remote Similarity NPC279026
0.5909 Remote Similarity NPC261080
0.5909 Remote Similarity NPC201844
0.5897 Remote Similarity NPC241404
0.5897 Remote Similarity NPC302611
0.5897 Remote Similarity NPC198126
0.5882 Remote Similarity NPC181153
0.587 Remote Similarity NPC228782
0.587 Remote Similarity NPC313565
0.587 Remote Similarity NPC259982
0.5854 Remote Similarity NPC57499
0.5849 Remote Similarity NPC6883
0.5814 Remote Similarity NPC321569
0.5769 Remote Similarity NPC277878
0.575 Remote Similarity NPC307739
0.575 Remote Similarity NPC76217
0.575 Remote Similarity NPC328569
0.5714 Remote Similarity NPC191084
0.5714 Remote Similarity NPC168052
0.5714 Remote Similarity NPC185768
0.5714 Remote Similarity NPC316685
0.5714 Remote Similarity NPC250870
0.5714 Remote Similarity NPC179624
0.5676 Remote Similarity NPC3343
0.5676 Remote Similarity NPC230726
0.5676 Remote Similarity NPC314668
0.566 Remote Similarity NPC196612
0.5652 Remote Similarity NPC149184
0.5652 Remote Similarity NPC171736
0.5652 Remote Similarity NPC209970
0.5652 Remote Similarity NPC325452
0.5652 Remote Similarity NPC216630
0.5652 Remote Similarity NPC163746
0.5652 Remote Similarity NPC196924
0.5652 Remote Similarity NPC307783
0.5652 Remote Similarity NPC248763
0.5652 Remote Similarity NPC103286
0.5641 Remote Similarity NPC270334
0.5625 Remote Similarity NPC270088
0.5614 Remote Similarity NPC17935
0.561 Remote Similarity NPC286695
0.561 Remote Similarity NPC108238
0.561 Remote Similarity NPC94196
0.56 Remote Similarity NPC172086
0.56 Remote Similarity NPC247546

  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 NPC317945 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
0.8571 High Similarity NPD8857 Approved
0.7941 Intermediate Similarity NPD62 Approved
0.7222 Intermediate Similarity NPD8590 Approved
0.7143 Intermediate Similarity NPD8594 Approved
0.7143 Intermediate Similarity NPD8593 Approved
0.7059 Intermediate Similarity NPD8189 Approved
0.6596 Remote Similarity NPD9122 Approved
0.6596 Remote Similarity NPD9124 Approved
0.6596 Remote Similarity NPD108 Approved
0.6596 Remote Similarity NPD9123 Approved
0.6596 Remote Similarity NPD70 Approved
0.6596 Remote Similarity NPD9128 Approved
0.6596 Remote Similarity NPD9130 Phase 3
0.6596 Remote Similarity NPD9127 Approved
0.6596 Remote Similarity NPD9121 Approved
0.6596 Remote Similarity NPD109 Approved
0.6596 Remote Similarity NPD9125 Approved
0.6458 Remote Similarity NPD9126 Approved
0.6458 Remote Similarity NPD9129 Approved
0.6458 Remote Similarity NPD71 Approved
0.6389 Remote Similarity NPD106 Approved
0.6364 Remote Similarity NPD8604 Approved
0.6364 Remote Similarity NPD8603 Approved
0.6364 Remote Similarity NPD8599 Approved
0.6364 Remote Similarity NPD8600 Approved
0.6364 Remote Similarity NPD8605 Approved
0.6364 Remote Similarity NPD8601 Approved
0.6364 Remote Similarity NPD8598 Approved
0.6364 Remote Similarity NPD8602 Approved
0.6286 Remote Similarity NPD8591 Approved
0.6286 Remote Similarity NPD8592 Approved
0.6098 Remote Similarity NPD8596 Approved
0.6053 Remote Similarity NPD8619 Approved
0.6053 Remote Similarity NPD8617 Approved
0.6042 Remote Similarity NPD8867 Approved
0.6042 Remote Similarity NPD8866 Approved
0.6 Remote Similarity NPD9116 Phase 1
0.5952 Remote Similarity NPD8597 Approved
0.5909 Remote Similarity NPD77 Approved
0.5909 Remote Similarity NPD9448 Phase 2
0.5909 Remote Similarity NPD9655 Approved
0.5909 Remote Similarity NPD9450 Approved
0.5909 Remote Similarity NPD633 Phase 3
0.5897 Remote Similarity NPD8618 Approved
0.5882 Remote Similarity NPD8201 Phase 2
0.5882 Remote Similarity NPD8616 Clinical (unspecified phase)
0.5882 Remote Similarity NPD8615 Phase 2
0.5882 Remote Similarity NPD8190 Phase 2
0.5778 Remote Similarity NPD9635 Discontinued
0.5769 Remote Similarity NPD9009 Approved
0.5769 Remote Similarity NPD72 Approved
0.5769 Remote Similarity NPD9007 Approved
0.5769 Remote Similarity NPD65 Approved
0.5769 Remote Similarity NPD9010 Approved
0.5769 Remote Similarity NPD64 Approved
0.5769 Remote Similarity NPD66 Approved
0.5769 Remote Similarity NPD8960 Approved
0.5769 Remote Similarity NPD9011 Approved
0.5769 Remote Similarity NPD9008 Approved
0.575 Remote Similarity NPD8202 Approved
0.575 Remote Similarity NPD8205 Approved
0.5652 Remote Similarity NPD2270 Approved
0.56 Remote Similarity NPD9003 Clinical (unspecified phase)
0.56 Remote Similarity NPD9004 Approved
0.56 Remote Similarity NPD9005 Phase 3

  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