Structure

Physi-Chem Properties

Molecular Weight:  160.05
Volume:  138.361
LogP:  -2.131
LogD:  -1.62
LogS:  -0.055
# Rotatable Bonds:  2
TPSA:  112.48
# H-Bond Aceptor:  6
# H-Bond Donor:  5
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.384
Synthetic Accessibility Score:  4.119
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.204
MDCK Permeability:  0.006406250409781933
Pgp-inhibitor:  0.0
Pgp-substrate:  0.288
Human Intestinal Absorption (HIA):  0.045
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.66
Plasma Protein Binding (PPB):  12.547954559326172%
Volume Distribution (VD):  0.593
Pgp-substrate:  82.80623626708984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.069
CYP2C19-inhibitor:  0.046
CYP2C19-substrate:  0.059
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.313
CYP2D6-inhibitor:  0.06
CYP2D6-substrate:  0.189
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.06

ADMET: Excretion

Clearance (CL):  2.258
Half-life (T1/2):  0.871

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.431
Drug-inuced Liver Injury (DILI):  0.66
AMES Toxicity:  0.771
Rat Oral Acute Toxicity:  0.735
Maximum Recommended Daily Dose:  0.021
Skin Sensitization:  0.384
Carcinogencity:  0.835
Eye Corrosion:  0.003
Eye Irritation:  0.018
Respiratory Toxicity:  0.954

Download Data

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

  Natural Product: NPC118524

Natural Product ID:  NPC118524
Common Name*:   L-Erythro-Tricholomic Acid
IUPAC Name:   (2S)-2-amino-2-[(5S)-3-oxo-1,2-oxazolidin-5-yl]acetic acid
Synonyms:  
Standard InCHIKey:  NTHMUJMQOXQYBR-OKKQSCSOSA-N
Standard InCHI:  InChI=1S/C5H8N2O4/c6-4(5(9)10)2-1-3(8)7-11-2/h2,4H,1,6H2,(H,7,8)(H,9,10)/t2-,4-/m0/s1
SMILES:  OC(=O)[C@H]([C@H]1ON=C(C1)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL260328
PubChem CID:   441456
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:0002404] Alpha amino acids
                • [CHEMONTID:0004146] L-alpha-amino 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
NPO1517 Crotalaria tetragona Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1517 Crotalaria tetragona Species Fabaceae 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
NPT3750 Individual Protein Glutamate receptor ionotropic, AMPA 1 Rattus norvegicus EC50 = 120000.0 nM PMID[552006]
NPT3750 Individual Protein Glutamate receptor ionotropic, AMPA 1 Rattus norvegicus EC50 = 114815.36 nM PMID[552006]
NPT3750 Individual Protein Glutamate receptor ionotropic, AMPA 1 Rattus norvegicus Activity = 90.0 % PMID[552006]
NPT3751 Individual Protein Glutamate receptor ionotropic, AMPA 2 Rattus norvegicus EC50 = 480000.0 nM PMID[552006]
NPT3751 Individual Protein Glutamate receptor ionotropic, AMPA 2 Rattus norvegicus EC50 = 2238721138568.34 nM PMID[552006]
NPT3751 Individual Protein Glutamate receptor ionotropic, AMPA 2 Rattus norvegicus Activity = 74.0 % PMID[552006]
NPT3752 Individual Protein Glutamate receptor ionotropic, AMPA 3 Rattus norvegicus EC50 = 170000.0 nM PMID[552006]
NPT3752 Individual Protein Glutamate receptor ionotropic, AMPA 3 Rattus norvegicus EC50 = 154881.66 nM PMID[552006]
NPT3752 Individual Protein Glutamate receptor ionotropic, AMPA 3 Rattus norvegicus Activity = 88.0 % PMID[552006]
NPT3753 Individual Protein Glutamate receptor ionotropic, AMPA 4 Rattus norvegicus EC50 = 30000.0 nM PMID[552006]
NPT3753 Individual Protein Glutamate receptor ionotropic, AMPA 4 Rattus norvegicus EC50 = 29512.09 nM PMID[552006]
NPT3753 Individual Protein Glutamate receptor ionotropic, AMPA 4 Rattus norvegicus Activity = 91.0 % PMID[552006]
NPT3748 Individual Protein Glutamate receptor ionotropic kainate 1 Rattus norvegicus EC50 = 280000.0 nM PMID[552006]
NPT3748 Individual Protein Glutamate receptor ionotropic kainate 1 Rattus norvegicus EC50 = 251188.64 nM PMID[552006]
NPT3748 Individual Protein Glutamate receptor ionotropic kainate 1 Rattus norvegicus Activity = 91.0 % PMID[552006]
NPT3081 Individual Protein Metabotropic glutamate receptor 2 Rattus norvegicus EC50 > 1000000.0 nM PMID[552006]
NPT3738 Individual Protein Glutamate receptor ionotropic kainate 2 Rattus norvegicus EC50 = 82000.0 nM PMID[552006]
NPT3738 Individual Protein Glutamate receptor ionotropic kainate 2 Rattus norvegicus EC50 = 81283.05 nM PMID[552006]
NPT3738 Individual Protein Glutamate receptor ionotropic kainate 2 Rattus norvegicus Activity = 91.0 % PMID[552006]
NPT3080 Individual Protein Metabotropic glutamate receptor 1 Rattus norvegicus EC50 = 610000.0 nM PMID[552006]
NPT3080 Individual Protein Metabotropic glutamate receptor 1 Rattus norvegicus EC50 = 1737800828749.38 nM PMID[552006]
NPT3082 Individual Protein Metabotropic glutamate receptor 4 Rattus norvegicus EC50 > 1000000.0 nM PMID[552006]
NPT2 Others Unspecified IC50 = 950.0 nM PMID[552006]
NPT2 Others Unspecified IC50 = 954.99 nM PMID[552006]
NPT2 Others Unspecified IC50 = 290.0 nM PMID[552006]
NPT2 Others Unspecified IC50 = 281.84 nM PMID[552006]
NPT1496 Protein Complex Glutamate NMDA receptor Rattus norvegicus Ki = 41000.0 nM PMID[552006]
NPT1496 Protein Complex Glutamate NMDA receptor Rattus norvegicus Ki = 39810.72 nM PMID[552006]
NPT2 Others Unspecified IC50 = 281.84 nM PMID[552007]
NPT1496 Protein Complex Glutamate NMDA receptor Rattus norvegicus Ki = 39810.72 nM PMID[552007]
NPT2 Others Unspecified IC50 = 954.99 nM PMID[552007]
NPT1496 Protein Complex Glutamate NMDA receptor Rattus norvegicus Ki = 41000.0 nM PMID[552007]
NPT2 Others Unspecified IC50 = 290.0 nM PMID[552007]
NPT2 Others Unspecified IC50 = 950.0 nM PMID[552007]

☑ 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 NPC118524 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
0.7869 Intermediate Similarity NPC197087
0.7869 Intermediate Similarity NPC190184
0.7778 Intermediate Similarity NPC325985
0.75 Intermediate Similarity NPC38463
0.7424 Intermediate Similarity NPC321536
0.7344 Intermediate Similarity NPC322573
0.7313 Intermediate Similarity NPC143722
0.7143 Intermediate Similarity NPC19576
0.7143 Intermediate Similarity NPC29950
0.7059 Intermediate Similarity NPC68974
0.7031 Intermediate Similarity NPC329495
0.7 Intermediate Similarity NPC289691
0.6984 Remote Similarity NPC273330
0.6984 Remote Similarity NPC137958
0.6984 Remote Similarity NPC327239
0.6901 Remote Similarity NPC174304
0.6901 Remote Similarity NPC325597
0.6849 Remote Similarity NPC319046
0.6825 Remote Similarity NPC270805
0.6825 Remote Similarity NPC93888
0.6818 Remote Similarity NPC2801
0.6761 Remote Similarity NPC88898
0.6761 Remote Similarity NPC106216
0.6667 Remote Similarity NPC327542
0.6533 Remote Similarity NPC126779
0.6515 Remote Similarity NPC263065
0.6515 Remote Similarity NPC189178
0.6452 Remote Similarity NPC118459
0.6452 Remote Similarity NPC327698
0.6429 Remote Similarity NPC254541
0.6429 Remote Similarity NPC321468
0.6429 Remote Similarity NPC317143
0.6429 Remote Similarity NPC327748
0.6429 Remote Similarity NPC320598
0.6429 Remote Similarity NPC316826
0.6406 Remote Similarity NPC153370
0.6406 Remote Similarity NPC93081
0.6406 Remote Similarity NPC140872
0.6338 Remote Similarity NPC327170
0.6338 Remote Similarity NPC329564
0.6308 Remote Similarity NPC324825
0.6308 Remote Similarity NPC316231
0.6308 Remote Similarity NPC112890
0.6296 Remote Similarity NPC314680
0.6286 Remote Similarity NPC190385
0.6286 Remote Similarity NPC176164
0.6286 Remote Similarity NPC189301
0.625 Remote Similarity NPC136159
0.625 Remote Similarity NPC193386
0.625 Remote Similarity NPC181588
0.623 Remote Similarity NPC105488
0.619 Remote Similarity NPC329263
0.6176 Remote Similarity NPC60672
0.6176 Remote Similarity NPC322091
0.6164 Remote Similarity NPC327252
0.6143 Remote Similarity NPC318260
0.6143 Remote Similarity NPC317147
0.6133 Remote Similarity NPC325534
0.6111 Remote Similarity NPC471129
0.6094 Remote Similarity NPC297220
0.6087 Remote Similarity NPC327831
0.6081 Remote Similarity NPC145658
0.6076 Remote Similarity NPC55274
0.6061 Remote Similarity NPC43204
0.6061 Remote Similarity NPC226027
0.6061 Remote Similarity NPC245027
0.6061 Remote Similarity NPC84636
0.6061 Remote Similarity NPC174246
0.6061 Remote Similarity NPC162620
0.6061 Remote Similarity NPC62045
0.6056 Remote Similarity NPC93861
0.6056 Remote Similarity NPC43169
0.6056 Remote Similarity NPC112224
0.6056 Remote Similarity NPC327895
0.6 Remote Similarity NPC476248
0.5976 Remote Similarity NPC315780
0.5972 Remote Similarity NPC473599
0.5968 Remote Similarity NPC219143
0.5968 Remote Similarity NPC226265
0.5942 Remote Similarity NPC279661
0.5942 Remote Similarity NPC183845
0.5942 Remote Similarity NPC321118
0.5942 Remote Similarity NPC316889
0.5904 Remote Similarity NPC316242
0.5897 Remote Similarity NPC28348
0.5897 Remote Similarity NPC474298
0.5897 Remote Similarity NPC473985
0.5897 Remote Similarity NPC474299
0.5897 Remote Similarity NPC472579
0.5897 Remote Similarity NPC475808
0.5882 Remote Similarity NPC475542
0.5844 Remote Similarity NPC135539
0.5844 Remote Similarity NPC196359
0.5844 Remote Similarity NPC221764
0.5844 Remote Similarity NPC78312
0.5833 Remote Similarity NPC315535
0.5833 Remote Similarity NPC315131
0.5833 Remote Similarity NPC478017
0.5823 Remote Similarity NPC478256
0.5823 Remote Similarity NPC477642
0.5821 Remote Similarity NPC328378
0.5821 Remote Similarity NPC286989
0.5806 Remote Similarity NPC326992
0.5806 Remote Similarity NPC168375
0.5806 Remote Similarity NPC121517
0.5789 Remote Similarity NPC50047
0.5783 Remote Similarity NPC472594
0.5714 Remote Similarity NPC37681
0.5714 Remote Similarity NPC327985
0.5698 Remote Similarity NPC314466
0.5694 Remote Similarity NPC278209
0.5682 Remote Similarity NPC155670
0.5682 Remote Similarity NPC145748
0.5682 Remote Similarity NPC95478
0.5679 Remote Similarity NPC477641
0.5679 Remote Similarity NPC477643
0.5679 Remote Similarity NPC315897
0.5679 Remote Similarity NPC320865
0.5652 Remote Similarity NPC322946
0.5652 Remote Similarity NPC477729
0.5641 Remote Similarity NPC222327
0.5641 Remote Similarity NPC188231
0.5625 Remote Similarity NPC291186
0.5625 Remote Similarity NPC276294
0.5625 Remote Similarity NPC107645
0.5625 Remote Similarity NPC167986
0.5618 Remote Similarity NPC227051
0.5616 Remote Similarity NPC11433
0.5616 Remote Similarity NPC245346
0.5616 Remote Similarity NPC302003
0.5606 Remote Similarity NPC309658
0.56 Remote Similarity NPC118429

  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 NPC118524 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
0.8485 Intermediate Similarity NPD8842 Clinical (unspecified phase)
0.7869 Intermediate Similarity NPD8785 Approved
0.7538 Intermediate Similarity NPD9433 Approved
0.7143 Intermediate Similarity NPD61 Approved
0.7143 Intermediate Similarity NPD8847 Approved
0.7143 Intermediate Similarity NPD8846 Approved
0.6984 Remote Similarity NPD8872 Phase 3
0.6984 Remote Similarity NPD8871 Approved
0.6901 Remote Similarity NPD348 Approved
0.6849 Remote Similarity NPD337 Discontinued
0.6825 Remote Similarity NPD8624 Approved
0.6769 Remote Similarity NPD8851 Phase 1
0.6712 Remote Similarity NPD1429 Clinical (unspecified phase)
0.6712 Remote Similarity NPD886 Clinical (unspecified phase)
0.6622 Remote Similarity NPD4241 Registered
0.6533 Remote Similarity NPD4242 Approved
0.6515 Remote Similarity NPD9205 Approved
0.6515 Remote Similarity NPD9204 Approved
0.641 Remote Similarity NPD9109 Discontinued
0.6406 Remote Similarity NPD8614 Approved
0.6406 Remote Similarity NPD8809 Approved
0.6406 Remote Similarity NPD8808 Approved
0.6364 Remote Similarity NPD2262 Clinical (unspecified phase)
0.6308 Remote Similarity NPD9044 Approved
0.6286 Remote Similarity NPD9023 Clinical (unspecified phase)
0.6282 Remote Similarity NPD6944 Clinical (unspecified phase)
0.625 Remote Similarity NPD8810 Clinical (unspecified phase)
0.625 Remote Similarity NPD574 Approved
0.623 Remote Similarity NPD8198 Approved
0.623 Remote Similarity NPD8197 Approved
0.6164 Remote Similarity NPD575 Clinical (unspecified phase)
0.6133 Remote Similarity NPD8952 Approved
0.6061 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6061 Remote Similarity NPD9017 Approved
0.6061 Remote Similarity NPD9018 Approved
0.5968 Remote Similarity NPD8217 Clinical (unspecified phase)
0.5968 Remote Similarity NPD8216 Approved
0.5904 Remote Similarity NPD3160 Suspended
0.5875 Remote Similarity NPD1147 Phase 2
0.5867 Remote Similarity NPD1151 Approved
0.5844 Remote Similarity NPD8868 Approved
0.5844 Remote Similarity NPD2263 Discontinued
0.5833 Remote Similarity NPD7918 Clinical (unspecified phase)
0.5833 Remote Similarity NPD7917 Clinical (unspecified phase)
0.5814 Remote Similarity NPD1448 Clinical (unspecified phase)
0.575 Remote Similarity NPD9446 Approved
0.5745 Remote Similarity NPD8394 Approved
0.5679 Remote Similarity NPD1825 Clinical (unspecified phase)
0.5679 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5652 Remote Similarity NPD9441 Phase 2
0.5641 Remote Similarity NPD9421 Phase 1
0.5625 Remote Similarity NPD8804 Approved
0.5625 Remote Similarity NPD8805 Approved
0.5625 Remote Similarity NPD6428 Approved
0.5616 Remote Similarity NPD8865 Approved
0.561 Remote Similarity NPD366 Approved
0.5604 Remote Similarity NPD3177 Phase 3
0.56 Remote Similarity NPD9014 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