Structure

Physi-Chem Properties

Molecular Weight:  160.08
Volume:  155.424
LogP:  -1.625
LogD:  -1.059
LogS:  -0.178
# Rotatable Bonds:  5
TPSA:  69.64
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.541
Synthetic Accessibility Score:  2.262
Fsp3:  0.667
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:  -5.622
MDCK Permeability:  0.00012730152229778469
Pgp-inhibitor:  0.004
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.829
Plasma Protein Binding (PPB):  12.208080291748047%
Volume Distribution (VD):  0.43
Pgp-substrate:  83.65192413330078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.005
CYP1A2-substrate:  0.116
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.06
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.604
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.188
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.038

ADMET: Excretion

Clearance (CL):  5.467
Half-life (T1/2):  0.735

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.272
Drug-inuced Liver Injury (DILI):  0.086
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.131
Carcinogencity:  0.939
Eye Corrosion:  0.109
Eye Irritation:  0.817
Respiratory Toxicity:  0.025

Download Data

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

  Natural Product: NPC43264

Natural Product ID:  NPC43264
Common Name*:   Daminozide
IUPAC Name:   4-(2,2-dimethylhydrazinyl)-4-oxobutanoic acid
Synonyms:   N-(Dimethylamino)Succinamic Acid
Standard InCHIKey:  NOQGZXFMHARMLW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H12N2O3/c1-8(2)7-5(9)3-4-6(10)11/h3-4H2,1-2H3,(H,7,9)(H,10,11)
SMILES:  CN(N=C(CCC(=O)O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2164243
PubChem CID:   15331
72200802
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0000333] Straight chain fatty 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
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodchem.2009.03.042]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.3136/fstr.15.499]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/AJB10.140]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/AJB2010.000-3252]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers Tongxiang, China n.a. PMID[24621197]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. PMID[28248102]
NPO30745 Chrysanthemum morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[8158164]
NPO30745 Chrysanthemum morifolium Species Asteraceae Eukaryota n.a. inflorescence n.a. PMID[8158164]
NPO30745 Chrysanthemum morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30745 Chrysanthemum morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4728 Streptomyces tsukubensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO1899 Aria rostellata Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4706 Streptomyces vinaceusdrappus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO978 Panzerina lanata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6604 Melanothamnus afaqhusainii Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5641 Dendroctonus frontalis Species Curculionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2832 Hazunta membranacea n.a. n.a. n.a. 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
NPT2724 Individual Protein Lysine-specific demethylase 2A Homo sapiens Ki = 85000.0 nM PMID[561829]
NPT2724 Individual Protein Lysine-specific demethylase 2A Homo sapiens Ki = 1970.0 nM PMID[561829]
NPT2724 Individual Protein Lysine-specific demethylase 2A Homo sapiens IC50 = 1500.0 nM PMID[561829]
NPT2882 Individual Protein Gamma-butyrobetaine dioxygenase Homo sapiens IC50 > 100000.0 nM PMID[561829]
NPT2883 Individual Protein Egl nine homolog 1 Homo sapiens IC50 > 100000.0 nM PMID[561829]
NPT1599 Individual Protein Hypoxia-inducible factor 1-alpha inhibitor Homo sapiens IC50 > 100000.0 nM PMID[561829]
NPT2884 Individual Protein Lysine-specific demethylase 6B Homo sapiens IC50 > 100000.0 nM PMID[561829]
NPT2885 Individual Protein Lysine-specific demethylase 5C Homo sapiens IC50 > 100000.0 nM PMID[561829]
NPT48 Individual Protein Lysine-specific demethylase 4D-like Homo sapiens IC50 > 100000.0 nM PMID[561829]
NPT2886 Individual Protein Lysine-specific demethylase 7 Homo sapiens IC50 = 2100.0 nM PMID[561829]
NPT2887 Individual Protein Histone lysine demethylase PHF8 Homo sapiens IC50 = 550.0 nM PMID[561829]
NPT2888 Individual Protein Lysine-specific demethylase 6A Homo sapiens IC50 > 100000.0 nM PMID[561830]
NPT2724 Individual Protein Lysine-specific demethylase 2A Homo sapiens IC50 = 1500.0 nM PMID[561830]
NPT2887 Individual Protein Histone lysine demethylase PHF8 Homo sapiens IC50 = 550.0 nM PMID[561830]
NPT2889 Individual Protein Lysine-specific demethylase 5A Homo sapiens IC50 = 2200000.0 nM PMID[561830]
NPT2725 Individual Protein Lysine-specific demethylase 4C Homo sapiens IC50 = 2500000.0 nM PMID[561830]
NPT532 Individual Protein Lysine-specific demethylase 4A Homo sapiens IC50 > 3300000.0 nM PMID[561830]
NPT2887 Individual Protein Histone lysine demethylase PHF8 Homo sapiens IC50 = 19000.0 nM PMID[561830]
NPT49 Individual Protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 794.3 nM PMID[561833]
NPT2 Others Unspecified Ratio IC50 = 60.0 n.a. PMID[561829]
NPT2 Others Unspecified IC50 = 127000.0 nM PMID[561829]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Potency n.a. 1882.1 nM PMID[561831]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Potency n.a. 0.7 nM PMID[561831]
NPT610 Others Molecular identity unknown Potency n.a. 31622.8 nM PMID[561832]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Potency n.a. 9432.9 nM PMID[561831]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Potency n.a. 167.7 nM PMID[561831]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -4.94 % PMID[561834]
NPT22599 SINGLE PROTEIN Prolyl 4-hydroxylase Paramecium bursaria Chlorella virus 1 IC50 > 100000.0 nM PMID[561835]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 23.94 % PMID[561836]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 0.33 % PMID[561837]
NPT2 Others Unspecified Potency n.a. 27306 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 17373.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 8852.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 6859 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 24950.2 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 NPC43264 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
0.68 Remote Similarity NPC227850
0.68 Remote Similarity NPC153370
0.6522 Remote Similarity NPC327250
0.64 Remote Similarity NPC297220
0.6364 Remote Similarity NPC327831
0.6346 Remote Similarity NPC328378
0.6182 Remote Similarity NPC316889
0.6182 Remote Similarity NPC321118
0.6167 Remote Similarity NPC105297
0.6071 Remote Similarity NPC322573
0.6 Remote Similarity NPC149209
0.5968 Remote Similarity NPC128559
0.5965 Remote Similarity NPC38463
0.5909 Remote Similarity NPC260324
0.5902 Remote Similarity NPC327252
0.587 Remote Similarity NPC229838
0.5833 Remote Similarity NPC33721
0.5818 Remote Similarity NPC322946
0.5814 Remote Similarity NPC198126
0.5806 Remote Similarity NPC315744
0.5769 Remote Similarity NPC306238
0.5769 Remote Similarity NPC248970
0.5745 Remote Similarity NPC69179
0.5714 Remote Similarity NPC189178
0.5714 Remote Similarity NPC168375
0.5714 Remote Similarity NPC326992
0.5714 Remote Similarity NPC263065
0.5714 Remote Similarity NPC66043
0.5714 Remote Similarity NPC236709
0.5714 Remote Similarity NPC121517
0.5714 Remote Similarity NPC190184
0.5714 Remote Similarity NPC197087
0.5692 Remote Similarity NPC306696
0.569 Remote Similarity NPC313263
0.569 Remote Similarity NPC325985
0.5667 Remote Similarity NPC473599
0.5667 Remote Similarity NPC327748
0.5667 Remote Similarity NPC254541
0.5667 Remote Similarity NPC317143
0.5667 Remote Similarity NPC316826
0.5667 Remote Similarity NPC321468
0.566 Remote Similarity NPC136159
0.5652 Remote Similarity NPC316685
0.5636 Remote Similarity NPC327239
0.5636 Remote Similarity NPC329181
0.5636 Remote Similarity NPC319110
0.5625 Remote Similarity NPC18188
0.5625 Remote Similarity NPC470108

  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 NPC43264 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
0.68 Remote Similarity NPD8614 Approved
0.6531 Remote Similarity NPD9658 Clinical (unspecified phase)
0.6182 Remote Similarity NPD9419 Clinical (unspecified phase)
0.6 Remote Similarity NPD8869 Approved
0.6 Remote Similarity NPD574 Approved
0.5902 Remote Similarity NPD575 Clinical (unspecified phase)
0.5833 Remote Similarity NPD8576 Approved
0.5818 Remote Similarity NPD9441 Phase 2
0.5814 Remote Similarity NPD8618 Approved
0.5769 Remote Similarity NPD8870 Approved
0.5763 Remote Similarity NPD9433 Approved
0.5714 Remote Similarity NPD8785 Approved
0.5714 Remote Similarity NPD8593 Approved
0.5714 Remote Similarity NPD8594 Approved
0.5714 Remote Similarity NPD9204 Approved
0.5714 Remote Similarity NPD9205 Approved
0.566 Remote Similarity NPD1458 Approved
0.566 Remote Similarity NPD1459 Approved
0.5636 Remote Similarity NPD329 Discontinued
0.5625 Remote Similarity NPD8623 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