Structure

Physi-Chem Properties

Molecular Weight:  132.04
Volume:  124.924
LogP:  -0.037
LogD:  0.124
LogS:  -0.075
# Rotatable Bonds:  4
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.383
Synthetic Accessibility Score:  1.966
Fsp3:  0.6
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:  -4.619
MDCK Permeability:  0.00038252995000220835
Pgp-inhibitor:  0.003
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.97
Plasma Protein Binding (PPB):  17.322010040283203%
Volume Distribution (VD):  0.42
Pgp-substrate:  77.66666412353516%

ADMET: Metabolism

CYP1A2-inhibitor:  0.058
CYP1A2-substrate:  0.554
CYP2C19-inhibitor:  0.048
CYP2C19-substrate:  0.521
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.127
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.224
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.288

ADMET: Excretion

Clearance (CL):  8.236
Half-life (T1/2):  0.919

ADMET: Toxicity

hERG Blockers:  0.035
Human Hepatotoxicity (H-HT):  0.142
Drug-inuced Liver Injury (DILI):  0.394
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.056
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.836
Carcinogencity:  0.166
Eye Corrosion:  0.993
Eye Irritation:  0.992
Respiratory Toxicity:  0.505

Download Data

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

  Natural Product: NPC55956

Natural Product ID:  NPC55956
Common Name*:   Dimethyl malonate
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BEPAFCGSDWSTEL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H8O4/c1-8-4(6)3-5(7)9-2/h3H2,1-2H3
SMILES:  COC(=O)CC(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000346] Dicarboxylic acids and derivatives

*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
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15670 Ananas comosus Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15670 Ananas comosus Species Bromeliaceae 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
NPO15670 NPC55956 Raw Fruit 0.006 0.006 0.006 mg/100g Database [DUKE]

☑ 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
NPT370 Cell Line NCI-H23 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT368 Cell Line SN12C Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT369 Cell Line ACHN Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT371 Cell Line UO-31 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT116 Cell Line HL-60 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT372 Cell Line HOP-92 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT374 Cell Line SF-539 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT375 Cell Line Malme-3M Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT373 Cell Line SK-MEL-5 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT111 Cell Line K562 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT376 Cell Line A498 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT377 Cell Line OVCAR-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT379 Cell Line HOP-62 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT112 Cell Line MOLT-4 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT380 Cell Line U-251 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT381 Cell Line OVCAR-8 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT382 Cell Line OVCAR-5 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT572 Cell Line DMS-273 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT383 Cell Line SNB-19 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT384 Cell Line TK-10 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT573 Cell Line M19-MEL Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT323 Cell Line SW-620 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT387 Cell Line M14 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT574 Cell Line XF498 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT386 Cell Line KM12 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT388 Cell Line NCI-H322M Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT456 Cell Line OVCAR-4 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT389 Cell Line RPMI-8226 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT390 Cell Line LOX IMVI Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT147 Cell Line SK-MEL-2 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT575 Cell Line KM-20L2 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT81 Cell Line A549 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT392 Cell Line SNB-75 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT391 Cell Line HCC 2998 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT148 Cell Line HCT-15 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT393 Cell Line HCT-116 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT395 Cell Line SF-268 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT394 Cell Line EKVX Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT731 Cell Line LXFL 529 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT576 Cell Line DMS-114 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT146 Cell Line SK-OV-3 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT398 Cell Line UACC-62 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT397 Cell Line NCI-H460 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT308 Cell Line CAKI-1 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT399 Cell Line SF-295 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT577 Cell Line RXF 631 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT458 Cell Line IGROV-1 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT578 Cell Line SNB-78 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT401 Cell Line 786-0 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT579 Cell Line DLD-1 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT403 Cell Line UACC-257 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT404 Cell Line CCRF-CEM Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT139 Cell Line HT-29 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT406 Cell Line RXF 393 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT732 Cell Line HOP-18 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT407 Cell Line COLO 205 Homo sapiens GI50 n.a. 100000.0 nM PMID[564744]
NPT2 Others Unspecified Potency n.a. 64233.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 4896.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 5494.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 56706.4 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 NPC55956 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
0.9286 High Similarity NPC265882
0.8077 Intermediate Similarity NPC8187
0.8 Intermediate Similarity NPC302611
0.7742 Intermediate Similarity NPC328569
0.75 Intermediate Similarity NPC32280
0.75 Intermediate Similarity NPC41485
0.75 Intermediate Similarity NPC28246
0.7419 Intermediate Similarity NPC241404
0.7407 Intermediate Similarity NPC203105
0.7241 Intermediate Similarity NPC166804
0.7241 Intermediate Similarity NPC3343
0.7143 Intermediate Similarity NPC110107
0.7097 Intermediate Similarity NPC180423
0.7 Intermediate Similarity NPC143211
0.6897 Remote Similarity NPC3693
0.6786 Remote Similarity NPC23508
0.6667 Remote Similarity NPC201132
0.6667 Remote Similarity NPC281883
0.6667 Remote Similarity NPC127134
0.6667 Remote Similarity NPC211250
0.6571 Remote Similarity NPC191084
0.6571 Remote Similarity NPC168052
0.6571 Remote Similarity NPC250870
0.6562 Remote Similarity NPC127696
0.6538 Remote Similarity NPC137050
0.6471 Remote Similarity NPC217218
0.6471 Remote Similarity NPC108238
0.6452 Remote Similarity NPC248233
0.6364 Remote Similarity NPC320981
0.6364 Remote Similarity NPC5934
0.6364 Remote Similarity NPC21374
0.6296 Remote Similarity NPC37493
0.6286 Remote Similarity NPC57499
0.625 Remote Similarity NPC281943
0.625 Remote Similarity NPC317739
0.625 Remote Similarity NPC88135
0.6207 Remote Similarity NPC208021
0.6176 Remote Similarity NPC12904
0.6129 Remote Similarity NPC230726
0.6129 Remote Similarity NPC314668
0.6129 Remote Similarity NPC149209
0.6071 Remote Similarity NPC260610
0.6061 Remote Similarity NPC232172
0.6061 Remote Similarity NPC312003
0.6 Remote Similarity NPC322892
0.6 Remote Similarity NPC35371
0.6 Remote Similarity NPC41007
0.6 Remote Similarity NPC286695
0.6 Remote Similarity NPC8368
0.6 Remote Similarity NPC178643
0.6 Remote Similarity NPC168714
0.5946 Remote Similarity NPC159089
0.5862 Remote Similarity NPC181153
0.5833 Remote Similarity NPC154396
0.5833 Remote Similarity NPC140229
0.5806 Remote Similarity NPC35155
0.5789 Remote Similarity NPC206924
0.5758 Remote Similarity NPC234005
0.5714 Remote Similarity NPC228727
0.5714 Remote Similarity NPC40965
0.5676 Remote Similarity NPC325165
0.5676 Remote Similarity NPC155872
0.5667 Remote Similarity NPC2419
0.5667 Remote Similarity NPC185768
0.561 Remote Similarity NPC35661

  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 NPC55956 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
0.7692 Intermediate Similarity NPD8191 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD106 Approved
0.6897 Remote Similarity NPD8188 Approved
0.6667 Remote Similarity NPD8989 Approved
0.6667 Remote Similarity NPD9636 Phase 2
0.6538 Remote Similarity NPD8200 Phase 2
0.6429 Remote Similarity NPD8616 Clinical (unspecified phase)
0.6429 Remote Similarity NPD8615 Phase 2
0.6364 Remote Similarity NPD8590 Approved
0.6364 Remote Similarity NPD8856 Phase 2
0.6286 Remote Similarity NPD900 Approved
0.5938 Remote Similarity NPD8990 Clinical (unspecified phase)
0.5862 Remote Similarity NPD8201 Phase 2
0.5806 Remote Similarity NPD8591 Approved
0.5806 Remote Similarity NPD8592 Approved
0.5789 Remote Similarity NPD9113 Discontinued
0.5789 Remote Similarity NPD9111 Approved
0.5789 Remote Similarity NPD9117 Approved
0.5676 Remote Similarity NPD9136 Clinical (unspecified phase)
0.561 Remote Similarity NPD9116 Phase 1

  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