Natural Product: NPC3343

Natural Product ID:  NPC3343
Common Name:   Malonic Acid
IUPAC Name:   propanedioic acid
Synonyms:  
Molecular Formula:   C3H4O4
Standard InCHIKey:  OFOBLEOULBTSOW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)
Canonical SMILES:  OC(=O)CC(=O)O
First Find Year:  
Max Developmental Stage:  
Synthetic Gene Cluster:   ;

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO1797 Homo sapiens Species Hominidae Eukaryota blood PMID[19403942]
NPO1797 Homo sapiens Species Hominidae Eukaryota urine PMID[24023812]
NPO1797 Homo sapiens Species Hominidae Eukaryota Faeces PMID[24029555]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota TCM_Taiwan*
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota TCM_Taiwan*
NPO26721 Apium graveolens Species Apiaceae Eukaryota TCM_Taiwan*
NPO29553 Hordei fructus germinatus NA NA NA TCMSP*
NPO298 Isatdis radix NA NA NA TCMSP*
NPO29141 Panax ginseng Species Araliaceae Eukaryota TCMSP*
NPO19707 Gynostemmae pentaphylli herba NA NA NA TCMSP*
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota TM-MC*
NPO11438 Angelica gigas Species Apiaceae Eukaryota TM-MC*
NPO15462 Angelica sinensis Species Apiaceae Eukaryota TM-MC*
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota TM-MC*
NPO28169 Aleurites cordata Species Euphorbiaceae Eukaryota TCMID*
NPO26721 Apium graveolens Species Apiaceae Eukaryota TCMID*
NPO12934 Gynostemma pentaphyllum Species Cucurbitaceae Eukaryota TCMID*
NPO993 Phaseolus coccineus Species Fabaceae Eukaryota TCMID*
NPO25583 Beta vulgaris Species Chenopodiaceae Eukaryota TCMID*
NPO87 Alchornea trewioides Species Euphorbiaceae Eukaryota TCMID*
NPO26880 Mallotus japonicus Species Euphorbiaceae Eukaryota TCMID*
NPO22132 Hordeum vulgare Species Poaceae Eukaryota TCMID*
NPO16506 Synotis alata Species Asteraceae Eukaryota UNPD*
NPO4305 Pertusaria wulfenii Species Pertusariaceae Eukaryota UNPD*
NPO12934 Gynostemma pentaphyllum Species Cucurbitaceae Eukaryota UNPD*
NPO11990 Coleostephus myconis Species Asteraceae Eukaryota UNPD*
NPO918 Dahlia pinnata Species Asteraceae Eukaryota UNPD*
NPO12934 Gynostemma pentaphyllum Species Cucurbitaceae Eukaryota TCM_Taiwan*
NPO1797 Homo sapiens Species Hominidae Eukaryota saliva DOI[10.1007/s11306-012-0464-y]
NPO1797 Homo sapiens Species Hominidae Eukaryota DOI[10.1038/nbt.2488]

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT36 Individual Protein Tyrosine-protein kinase SRC Homo sapiens IC50 > 40000000 nM 14613321
NPT643 Individual Protein Serine racemase Mus musculus Ki = 71000 nM 19791805
NPT644 Individual Protein L-lactate dehydrogenase A chain Homo sapiens Kd = 5000000 nM 22417091
NPT646 Individual Protein Serine racemase Homo sapiens IC50 = 24900 nM 23391306
NPT647 Individual Protein D-aspartate oxidase Homo sapiens IC50 = 1355000 nM 23391306
NPT645 Individual Protein D-amino-acid oxidase Homo sapiens IC50 > 10000000 nM 23391306
NPT2 Others Unspecified Potency 56234.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency 43753.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency 386.5 nM PubChem BioAssay data set
NPT643 Individual Protein Serine racemase Mus musculus Ki = 27000 nM 25462239
NPT643 Individual Protein Serine racemase Mus musculus IC50 = 67000 nM 25462239
NPT646 Individual Protein Serine racemase Homo sapiens Inhibition = 59 % 25066953
NPT646 Individual Protein Serine racemase Homo sapiens IC50 = 1310000 nM 25066953
NPT646 Individual Protein Serine racemase Homo sapiens Ki = 33000 nM 25066953
NPT2 Others Unspecified Potency 61803.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency 490.9 nM PubChem BioAssay data set
NPT163 Individual Protein Nuclear factor NF-kappa-B p105 subunit Homo sapiens Potency 9795.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency 54593.5 nM PubChem BioAssay data set
NPT646 Individual Protein Serine racemase Homo sapiens Ki = 59000 nM 26283510
NPT646 Individual Protein Serine racemase Homo sapiens Ki = 66000 nM 26283510
NPT646 Individual Protein Serine racemase Homo sapiens Inhibition = 76 % 26283510
NPT648 Individual Protein D-aspartate oxidase Mus musculus Ki = 1220000 nM 26322531
NPT649 Individual Protein D-aspartate oxidase Rattus norvegicus Ki = 1562000 nM 26322531
NPT647 Individual Protein D-aspartate oxidase Homo sapiens Ki = 153000 nM 26322531
NPT645 Individual Protein D-amino-acid oxidase Homo sapiens IC50 > 10000000 nM 26322531
NPT647 Individual Protein D-aspartate oxidase Homo sapiens IC50 = 879000 nM 26322531

  Similar Natural Products 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 NPC3343 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
0.8571 High Similarity NPC241404
0.8276 Intermediate Similarity NPC328569
0.76 Intermediate Similarity NPC181153
0.7333 Intermediate Similarity NPC320981
0.7273 Intermediate Similarity NPC159089
0.7241 Intermediate Similarity NPC55956
0.6774 Remote Similarity NPC265882
0.6765 Remote Similarity NPC1037
0.6667 Remote Similarity NPC236709
0.6552 Remote Similarity NPC230726
0.6552 Remote Similarity NPC286233
0.6552 Remote Similarity NPC314668
0.6552 Remote Similarity NPC149209
0.6471 Remote Similarity NPC191084
0.6471 Remote Similarity NPC250870
0.6471 Remote Similarity NPC168052
0.64 Remote Similarity NPC68873
0.6333 Remote Similarity NPC320704
0.625 Remote Similarity NPC16947
0.5938 Remote Similarity NPC122768
0.5938 Remote Similarity NPC61066
0.5938 Remote Similarity NPC151140
0.5938 Remote Similarity NPC174368
0.5938 Remote Similarity NPC292641
0.5938 Remote Similarity NPC104195
0.5897 Remote Similarity NPC24751
0.5897 Remote Similarity NPC97444
0.5897 Remote Similarity NPC100742
0.5897 Remote Similarity NPC121018
0.5897 Remote Similarity NPC325307
0.5897 Remote Similarity NPC322956
0.5897 Remote Similarity NPC192402
0.5897 Remote Similarity NPC35661
0.5897 Remote Similarity NPC19044
0.5882 Remote Similarity NPC125575
0.5882 Remote Similarity NPC18224
0.5882 Remote Similarity NPC328710
0.5769 Remote Similarity NPC7922
0.5769 Remote Similarity NPC283245
0.5758 Remote Similarity NPC198126
0.5758 Remote Similarity NPC302611
0.575 Remote Similarity NPC310220
0.575 Remote Similarity NPC107645
0.5676 Remote Similarity NPC317945
0.561 Remote Similarity NPC320624

  Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC3343 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
0.8333 Intermediate Similarity NPD8191 Clinical (unspecified phase)
0.76 Intermediate Similarity NPD8201 Phase 2
0.7333 Intermediate Similarity NPD8590 Approved
0.6667 Remote Similarity NPD8593 Approved
0.6667 Remote Similarity NPD8594 Approved
0.6552 Remote Similarity NPD8189 Approved
0.64 Remote Similarity NPD7364 Approved
0.64 Remote Similarity NPD8200 Phase 2
0.6333 Remote Similarity NPD106 Approved
0.6316 Remote Similarity NPD9116 Phase 1
0.6207 Remote Similarity NPD8188 Approved
0.5938 Remote Similarity NPD8619 Approved
0.5938 Remote Similarity NPD8617 Approved
0.5897 Remote Similarity NPD8603 Approved
0.5897 Remote Similarity NPD8605 Approved
0.5897 Remote Similarity NPD8604 Approved
0.5897 Remote Similarity NPD8601 Approved
0.5897 Remote Similarity NPD8600 Approved
0.5897 Remote Similarity NPD8602 Approved
0.5897 Remote Similarity NPD8598 Approved
0.5897 Remote Similarity NPD8599 Approved
0.5758 Remote Similarity NPD8618 Approved
0.5714 Remote Similarity NPD8616 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8615 Phase 2
0.5676 Remote Similarity NPD9111 Approved
0.5676 Remote Similarity NPD9113 Discontinued
0.5676 Remote Similarity NPD9117 Approved
0.5667 Remote Similarity NPD8591 Approved
0.5667 Remote Similarity NPD8592 Approved

Structure

External Identifiers

PubChem CID   867;23511544
ChEMBL   CHEMBL7942
ZINC  

Physicochemical Properties

Molecular Weight:  104.01
ALogP:  -0.4448
MLogP:  1.35
XLogP:  -0.299
# Rotatable Bonds:  4
Polar Surface Area:  74.6
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  7

Download Data

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