Structure

Physi-Chem Properties

Molecular Weight:  189.06
Volume:  176.667
LogP:  -1.098
LogD:  -0.734
LogS:  -0.933
# Rotatable Bonds:  6
TPSA:  103.7
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.537
Synthetic Accessibility Score:  2.228
Fsp3:  0.571
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:  -6.137
MDCK Permeability:  0.002400793833658099
Pgp-inhibitor:  0.0
Pgp-substrate:  0.062
Human Intestinal Absorption (HIA):  0.327
20% Bioavailability (F20%):  0.031
30% Bioavailability (F30%):  0.047

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.283
Plasma Protein Binding (PPB):  14.273216247558594%
Volume Distribution (VD):  0.245
Pgp-substrate:  79.4433822631836%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.035
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.038
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.82
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.114
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.003

ADMET: Excretion

Clearance (CL):  1.805
Half-life (T1/2):  0.812

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.059
Drug-inuced Liver Injury (DILI):  0.082
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.008
Skin Sensitization:  0.105
Carcinogencity:  0.041
Eye Corrosion:  0.012
Eye Irritation:  0.123
Respiratory Toxicity:  0.02

Download Data

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

  Natural Product: NPC189178

Natural Product ID:  NPC189178
Common Name*:   Aceglumate
IUPAC Name:   2-acetamidopentanedioic acid
Synonyms:  
Standard InCHIKey:  RFMMMVDNIPUKGG-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H11NO5/c1-4(9)8-5(7(12)13)2-3-6(10)11/h5H,2-3H2,1H3,(H,8,9)(H,10,11)(H,12,13)
SMILES:  CC(=NC(CCC(=O)O)C(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2142890
PubChem CID:   185
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0004323] Glutamic acid 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
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26429 Capsella bursa-pastoris Species Brassicaceae 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
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 115.8 nM PMID[558692]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 7079.5 nM PMID[558692]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM PMID[558693]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM PMID[558693]

☑ 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 NPC189178 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
1.0 High Similarity NPC263065
0.8846 High Similarity NPC322573
0.8421 Intermediate Similarity NPC327252
0.8393 Intermediate Similarity NPC143722
0.8333 Intermediate Similarity NPC325985
0.8333 Intermediate Similarity NPC38463
0.8269 Intermediate Similarity NPC29950
0.8269 Intermediate Similarity NPC19576
0.8077 Intermediate Similarity NPC273330
0.8077 Intermediate Similarity NPC137958
0.7925 Intermediate Similarity NPC322946
0.7895 Intermediate Similarity NPC321536
0.7818 Intermediate Similarity NPC2801
0.7778 Intermediate Similarity NPC197087
0.7778 Intermediate Similarity NPC190184
0.7736 Intermediate Similarity NPC327239
0.7377 Intermediate Similarity NPC289691
0.7358 Intermediate Similarity NPC227850
0.7258 Intermediate Similarity NPC174304
0.7258 Intermediate Similarity NPC325597
0.7241 Intermediate Similarity NPC317147
0.7241 Intermediate Similarity NPC318260
0.7119 Intermediate Similarity NPC176164
0.7119 Intermediate Similarity NPC189301
0.7115 Intermediate Similarity NPC118459
0.7115 Intermediate Similarity NPC327698
0.7 Intermediate Similarity NPC321468
0.7 Intermediate Similarity NPC316826
0.7 Intermediate Similarity NPC254541
0.7 Intermediate Similarity NPC317143
0.7 Intermediate Similarity NPC327748
0.6923 Remote Similarity NPC319046
0.6909 Remote Similarity NPC328378
0.6885 Remote Similarity NPC327170
0.6885 Remote Similarity NPC329564
0.6875 Remote Similarity NPC325534
0.6818 Remote Similarity NPC126779
0.6721 Remote Similarity NPC320598
0.6667 Remote Similarity NPC248970
0.6667 Remote Similarity NPC297220
0.6667 Remote Similarity NPC306238
0.6607 Remote Similarity NPC43204
0.6607 Remote Similarity NPC84636
0.6607 Remote Similarity NPC245027
0.6607 Remote Similarity NPC174246
0.6607 Remote Similarity NPC62045
0.6607 Remote Similarity NPC162620
0.6607 Remote Similarity NPC226027
0.6562 Remote Similarity NPC88898
0.6562 Remote Similarity NPC106216
0.6515 Remote Similarity NPC118524
0.6481 Remote Similarity NPC329263
0.6471 Remote Similarity NPC327250
0.6462 Remote Similarity NPC50047
0.6441 Remote Similarity NPC321118
0.6441 Remote Similarity NPC316889
0.6429 Remote Similarity NPC93081
0.6429 Remote Similarity NPC140872
0.6389 Remote Similarity NPC59867
0.6346 Remote Similarity NPC326992
0.6346 Remote Similarity NPC168375
0.6346 Remote Similarity NPC121517
0.6333 Remote Similarity NPC327831
0.6316 Remote Similarity NPC316231
0.6316 Remote Similarity NPC112890
0.6316 Remote Similarity NPC324825
0.6308 Remote Similarity NPC145658
0.6269 Remote Similarity NPC188231
0.6269 Remote Similarity NPC222327
0.625 Remote Similarity NPC260324
0.625 Remote Similarity NPC477644
0.625 Remote Similarity NPC125575
0.623 Remote Similarity NPC313263
0.6207 Remote Similarity NPC319110
0.6207 Remote Similarity NPC329181
0.619 Remote Similarity NPC473599
0.6167 Remote Similarity NPC183845
0.6167 Remote Similarity NPC279661
0.614 Remote Similarity NPC153370
0.6129 Remote Similarity NPC278209
0.6119 Remote Similarity NPC470108
0.6111 Remote Similarity NPC291186
0.6111 Remote Similarity NPC167986
0.6094 Remote Similarity NPC68974
0.6078 Remote Similarity NPC206924
0.6061 Remote Similarity NPC57420
0.6056 Remote Similarity NPC315897
0.6053 Remote Similarity NPC475542
0.6029 Remote Similarity NPC470109
0.6026 Remote Similarity NPC145748
0.6026 Remote Similarity NPC155670
0.6026 Remote Similarity NPC95478
0.6 Remote Similarity NPC329495
0.6 Remote Similarity NPC132307
0.6 Remote Similarity NPC325097
0.6 Remote Similarity NPC477642
0.6 Remote Similarity NPC478256
0.6 Remote Similarity NPC126925
0.5962 Remote Similarity NPC18188
0.5962 Remote Similarity NPC325454
0.5949 Remote Similarity NPC227051
0.5942 Remote Similarity NPC81647
0.5942 Remote Similarity NPC470110
0.5882 Remote Similarity NPC229838
0.5867 Remote Similarity NPC316242
0.5846 Remote Similarity NPC321419
0.5833 Remote Similarity NPC155156
0.5833 Remote Similarity NPC477643
0.5833 Remote Similarity NPC200550
0.5833 Remote Similarity NPC320865
0.5833 Remote Similarity NPC477641
0.5821 Remote Similarity NPC282178
0.5818 Remote Similarity NPC276294
0.5789 Remote Similarity NPC478017
0.5789 Remote Similarity NPC315535
0.5789 Remote Similarity NPC315131
0.5781 Remote Similarity NPC245346
0.5781 Remote Similarity NPC302003
0.5781 Remote Similarity NPC11433
0.5781 Remote Similarity NPC190385
0.5775 Remote Similarity NPC476291
0.5775 Remote Similarity NPC476285
0.5769 Remote Similarity NPC84128
0.5769 Remote Similarity NPC53858
0.5769 Remote Similarity NPC69179
0.5763 Remote Similarity NPC80350
0.5758 Remote Similarity NPC118429
0.5741 Remote Similarity NPC66043
0.5741 Remote Similarity NPC53449
0.5738 Remote Similarity NPC274499
0.5738 Remote Similarity NPC333075
0.5738 Remote Similarity NPC8488
0.5733 Remote Similarity NPC472594
0.5714 Remote Similarity NPC323974
0.5714 Remote Similarity NPC198301
0.5714 Remote Similarity NPC43264
0.5694 Remote Similarity NPC328457
0.5692 Remote Similarity NPC276928
0.5692 Remote Similarity NPC268927
0.5692 Remote Similarity NPC64250
0.569 Remote Similarity NPC101249
0.5667 Remote Similarity NPC198398
0.5667 Remote Similarity NPC27359
0.5667 Remote Similarity NPC295832
0.5667 Remote Similarity NPC319175
0.5667 Remote Similarity NPC315977
0.5658 Remote Similarity NPC314680
0.5634 Remote Similarity NPC472579
0.5634 Remote Similarity NPC474299
0.5634 Remote Similarity NPC28348
0.5634 Remote Similarity NPC474298
0.5634 Remote Similarity NPC473985
0.5634 Remote Similarity NPC475808
0.5625 Remote Similarity NPC174368
0.5616 Remote Similarity NPC141325
0.5614 Remote Similarity NPC208793
0.5614 Remote Similarity NPC285322
0.5606 Remote Similarity NPC177191

  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 NPC189178 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
1.0 High Similarity NPD9205 Approved
1.0 High Similarity NPD9204 Approved
0.8571 High Similarity NPD574 Approved
0.8421 Intermediate Similarity NPD575 Clinical (unspecified phase)
0.8364 Intermediate Similarity NPD9433 Approved
0.8269 Intermediate Similarity NPD8847 Approved
0.8269 Intermediate Similarity NPD8846 Approved
0.8269 Intermediate Similarity NPD61 Approved
0.8077 Intermediate Similarity NPD8871 Approved
0.8077 Intermediate Similarity NPD8872 Phase 3
0.7925 Intermediate Similarity NPD9441 Phase 2
0.7778 Intermediate Similarity NPD8851 Phase 1
0.7778 Intermediate Similarity NPD8785 Approved
0.7581 Intermediate Similarity NPD1429 Clinical (unspecified phase)
0.7302 Intermediate Similarity NPD886 Clinical (unspecified phase)
0.7258 Intermediate Similarity NPD348 Approved
0.6923 Remote Similarity NPD4241 Registered
0.6923 Remote Similarity NPD337 Discontinued
0.6875 Remote Similarity NPD8952 Approved
0.6866 Remote Similarity NPD2262 Clinical (unspecified phase)
0.6818 Remote Similarity NPD4242 Approved
0.6792 Remote Similarity NPD9658 Clinical (unspecified phase)
0.6765 Remote Similarity NPD6944 Clinical (unspecified phase)
0.6761 Remote Similarity NPD3160 Suspended
0.6667 Remote Similarity NPD8870 Approved
0.6607 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6607 Remote Similarity NPD9018 Approved
0.6607 Remote Similarity NPD9017 Approved
0.6522 Remote Similarity NPD1147 Phase 2
0.6491 Remote Similarity NPD329 Discontinued
0.6441 Remote Similarity NPD9419 Clinical (unspecified phase)
0.6429 Remote Similarity NPD8809 Approved
0.6429 Remote Similarity NPD8808 Approved
0.6316 Remote Similarity NPD9044 Approved
0.6269 Remote Similarity NPD9421 Phase 1
0.6184 Remote Similarity NPD1125 Discovery
0.614 Remote Similarity NPD8614 Approved
0.614 Remote Similarity NPD9214 Phase 3
0.614 Remote Similarity NPD9213 Approved
0.6111 Remote Similarity NPD8805 Approved
0.6111 Remote Similarity NPD8804 Approved
0.6104 Remote Similarity NPD7643 Phase 1
0.6056 Remote Similarity NPD1825 Clinical (unspecified phase)
0.6029 Remote Similarity NPD2263 Discontinued
0.6 Remote Similarity NPD8869 Approved
0.6 Remote Similarity NPD8798 Approved
0.5962 Remote Similarity NPD8623 Phase 1
0.5942 Remote Similarity NPD9451 Clinical (unspecified phase)
0.5915 Remote Similarity NPD9446 Approved
0.5857 Remote Similarity NPD3724 Clinical (unspecified phase)
0.5833 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5806 Remote Similarity NPD8971 Approved
0.5789 Remote Similarity NPD7918 Clinical (unspecified phase)
0.5789 Remote Similarity NPD8801 Approved
0.5789 Remote Similarity NPD7917 Clinical (unspecified phase)
0.5781 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5781 Remote Similarity NPD8865 Approved
0.5769 Remote Similarity NPD1448 Clinical (unspecified phase)
0.5763 Remote Similarity NPD8947 Approved
0.5763 Remote Similarity NPD8946 Approved
0.5758 Remote Similarity NPD9014 Approved
0.5753 Remote Similarity NPD9109 Discontinued
0.5753 Remote Similarity NPD366 Approved
0.5738 Remote Similarity NPD9386 Approved
0.5738 Remote Similarity NPD9420 Clinical (unspecified phase)
0.5714 Remote Similarity NPD9019 Approved
0.569 Remote Similarity NPD8850 Approved
0.569 Remote Similarity NPD8866 Approved
0.569 Remote Similarity NPD8867 Approved
0.5679 Remote Similarity NPD619 Phase 3
0.5667 Remote Similarity NPD9226 Approved
0.5667 Remote Similarity NPD9225 Phase 3
0.5614 Remote Similarity NPD8610 Approved

  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