Structure

Physi-Chem Properties

Molecular Weight:  156.05
Volume:  144.231
LogP:  -1.237
LogD:  -1.915
LogS:  0.02
# Rotatable Bonds:  3
TPSA:  86.21
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.481
Synthetic Accessibility Score:  3.46
Fsp3:  0.333
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:  -4.897
MDCK Permeability:  1.8045111573883332e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.774
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.391
30% Bioavailability (F30%):  0.086

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.623
Plasma Protein Binding (PPB):  20.54092025756836%
Volume Distribution (VD):  1.135
Pgp-substrate:  87.29227447509766%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.325
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.175
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.383
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.017
CYP3A4-inhibitor:  0.23
CYP3A4-substrate:  0.158

ADMET: Excretion

Clearance (CL):  2.553
Half-life (T1/2):  0.956

ADMET: Toxicity

hERG Blockers:  0.072
Human Hepatotoxicity (H-HT):  0.111
Drug-inuced Liver Injury (DILI):  0.931
AMES Toxicity:  0.19
Rat Oral Acute Toxicity:  0.278
Maximum Recommended Daily Dose:  0.031
Skin Sensitization:  0.881
Carcinogencity:  0.03
Eye Corrosion:  0.006
Eye Irritation:  0.835
Respiratory Toxicity:  0.153

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

  Natural Product: NPC174020

Natural Product ID:  NPC174020
Common Name*:   (S)-2-Hydroxy-3-(1H-Imidazol-4-Yl)Propanoic Acid
IUPAC Name:   (2S)-2-hydroxy-3-(1H-imidazol-5-yl)propanoic acid
Synonyms:  
Standard InCHIKey:  ACZFBYCNAVEFLC-YFKPBYRVSA-N
Standard InCHI:  InChI=1S/C6H8N2O3/c9-5(6(10)11)1-4-2-7-3-8-4/h2-3,5,9H,1H2,(H,7,8)(H,10,11)/t5-/m0/s1
SMILES:  O[C@H](C(=O)O)Cc1cnc[nH]1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3251663
PubChem CID:   440129
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000436] Azoles
        • [CHEMONTID:0000078] Imidazoles
          • [CHEMONTID:0002310] Substituted imidazoles
            • [CHEMONTID:0001227] Imidazolyl carboxylic 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
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. Antalya and Mugla Provinces, Turkey 200-Aug DOI[10.1016/j.scienta.2010.10.027]
NPO8884 Cuscuta reflexa Species Convolvulaceae Eukaryota n.a. whole plant n.a. PMID[11824569]
NPO19602 Nephelium maingayi Species Sapindaceae Eukaryota bark n.a. n.a. PMID[14987059]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. Cork, Ireland n.a. PMID[15223592]
NPO18559 Cucumaria okhotensis Species n.a. n.a. n.a. n.a. n.a. PMID[18288810]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[26562611]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8884 Cuscuta reflexa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8884 Cuscuta reflexa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18559 Cucumaria okhotensis Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO18991 Senecio candollei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19343 Centaurea glastifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19474 Clavaria pyxidata Species Clavariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17557 Hydrodictyon reticulatum Species Hydrodictyaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8884 Cuscuta reflexa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17305 Oenanthe phellandrium Species Muscicapidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15688 Astragalus oxyphysus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19673 Galanthus nivalis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19602 Nephelium maingayi Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19542 Grindelia havardii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14500 Pyrus pyraster Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19801 Euphorbia armena Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10029 Prunus dulcis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19214 Polyscias scutellaria Species Araliaceae 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
NPT4430 Individual Protein Histidine decarboxylase Rattus norvegicus Inhibition = 0.0 % PMID[469744]

☑ 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 NPC174020 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
0.9091 High Similarity NPC235501
0.8806 High Similarity NPC25465
0.8759 High Similarity NPC237812
0.8759 High Similarity NPC18223
0.8705 High Similarity NPC185903
0.8571 High Similarity NPC286696
0.8358 Intermediate Similarity NPC15566
0.8276 Intermediate Similarity NPC327477
0.8235 Intermediate Similarity NPC180462
0.8214 Intermediate Similarity NPC126634
0.8112 Intermediate Similarity NPC210947
0.7746 Intermediate Similarity NPC470138
0.7655 Intermediate Similarity NPC470140
0.7619 Intermediate Similarity NPC470139
0.75 Intermediate Similarity NPC60537
0.7353 Intermediate Similarity NPC327613
0.694 Remote Similarity NPC111132
0.6838 Remote Similarity NPC155498
0.6778 Remote Similarity NPC313504
0.6688 Remote Similarity NPC470141
0.6685 Remote Similarity NPC201900
0.6644 Remote Similarity NPC470142
0.6623 Remote Similarity NPC243319
0.6541 Remote Similarity NPC9639
0.6423 Remote Similarity NPC326248
0.6423 Remote Similarity NPC187191
0.6391 Remote Similarity NPC124276
0.6375 Remote Similarity NPC74306
0.6375 Remote Similarity NPC315642
0.6259 Remote Similarity NPC273327
0.6164 Remote Similarity NPC313547
0.6139 Remote Similarity NPC262926
0.6131 Remote Similarity NPC473646
0.6101 Remote Similarity NPC61198
0.6062 Remote Similarity NPC54537
0.604 Remote Similarity NPC238945
0.6036 Remote Similarity NPC282531
0.6 Remote Similarity NPC320818
0.5941 Remote Similarity NPC207633
0.5915 Remote Similarity NPC186619
0.5914 Remote Similarity NPC477118
0.5912 Remote Similarity NPC324009
0.5886 Remote Similarity NPC246193
0.5882 Remote Similarity NPC477120
0.5875 Remote Similarity NPC319221
0.5866 Remote Similarity NPC290959
0.5848 Remote Similarity NPC321052
0.5847 Remote Similarity NPC477119
0.5843 Remote Similarity NPC211820
0.5843 Remote Similarity NPC318590
0.5843 Remote Similarity NPC251233
0.5828 Remote Similarity NPC30326
0.5819 Remote Similarity NPC472790
0.5808 Remote Similarity NPC274384
0.5808 Remote Similarity NPC89147
0.5808 Remote Similarity NPC177169
0.5808 Remote Similarity NPC317746
0.58 Remote Similarity NPC63433
0.5798 Remote Similarity NPC315555
0.5783 Remote Similarity NPC8590
0.5782 Remote Similarity NPC323244
0.5775 Remote Similarity NPC293163
0.5774 Remote Similarity NPC232408
0.5774 Remote Similarity NPC64705
0.5774 Remote Similarity NPC197068
0.5758 Remote Similarity NPC209525
0.5758 Remote Similarity NPC161659
0.5752 Remote Similarity NPC327579
0.5748 Remote Similarity NPC328924
0.5735 Remote Similarity NPC282247
0.5731 Remote Similarity NPC326694
0.5714 Remote Similarity NPC239737
0.5714 Remote Similarity NPC89562
0.5698 Remote Similarity NPC324484
0.5689 Remote Similarity NPC314152
0.5684 Remote Similarity NPC313514
0.5667 Remote Similarity NPC41333
0.5667 Remote Similarity NPC325906
0.5655 Remote Similarity NPC59314
0.564 Remote Similarity NPC150853
0.5621 Remote Similarity NPC21448
0.5621 Remote Similarity NPC156461
0.5621 Remote Similarity NPC107374

  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 NPC174020 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
0.8759 High Similarity NPD9133 Approved
0.8489 Intermediate Similarity NPD9628 Approved
0.8451 Intermediate Similarity NPD9183 Clinical (unspecified phase)
0.8194 Intermediate Similarity NPD1451 Approved
0.8102 Intermediate Similarity NPD300 Approved
0.8092 Intermediate Similarity NPD3697 Discontinued
0.7959 Intermediate Similarity NPD9627 Approved
0.7931 Intermediate Similarity NPD875 Clinical (unspecified phase)
0.7548 Intermediate Similarity NPD1731 Clinical (unspecified phase)
0.75 Intermediate Similarity NPD2180 Approved
0.7405 Intermediate Similarity NPD2604 Approved
0.7222 Intermediate Similarity NPD3130 Discontinued
0.719 Intermediate Similarity NPD5342 Clinical (unspecified phase)
0.7117 Intermediate Similarity NPD5768 Phase 2
0.7078 Intermediate Similarity NPD568 Approved
0.7078 Intermediate Similarity NPD566 Approved
0.7078 Intermediate Similarity NPD567 Approved
0.7 Intermediate Similarity NPD9132 Discontinued
0.6941 Remote Similarity NPD3108 Clinical (unspecified phase)
0.694 Remote Similarity NPD8859 Approved
0.694 Remote Similarity NPD8861 Approved
0.694 Remote Similarity NPD8862 Approved
0.6923 Remote Similarity NPD3105 Discontinued
0.6752 Remote Similarity NPD3706 Clinical (unspecified phase)
0.6623 Remote Similarity NPD9081 Clinical (unspecified phase)
0.6622 Remote Similarity NPD1390 Phase 1
0.6622 Remote Similarity NPD1389 Clinical (unspecified phase)
0.6622 Remote Similarity NPD1388 Phase 1
0.6447 Remote Similarity NPD1807 Clinical (unspecified phase)
0.6375 Remote Similarity NPD582 Approved
0.6364 Remote Similarity NPD8271 Discontinued
0.6325 Remote Similarity NPD536 Clinical (unspecified phase)
0.6308 Remote Similarity NPD7465 Suspended
0.6203 Remote Similarity NPD576 Discontinued
0.6178 Remote Similarity NPD209 Clinical (unspecified phase)
0.6139 Remote Similarity NPD194 Clinical (unspecified phase)
0.6124 Remote Similarity NPD8119 Discontinued
0.6111 Remote Similarity NPD1430 Approved
0.6111 Remote Similarity NPD1431 Approved
0.6108 Remote Similarity NPD245 Suspended
0.6101 Remote Similarity NPD252 Clinical (unspecified phase)
0.609 Remote Similarity NPD9632 Phase 3
0.6084 Remote Similarity NPD775 Approved
0.6025 Remote Similarity NPD1808 Phase 1
0.6012 Remote Similarity NPD3708 Phase 2
0.6011 Remote Similarity NPD459 Clinical (unspecified phase)
0.6 Remote Similarity NPD8641 Approved
0.6 Remote Similarity NPD515 Phase 1
0.599 Remote Similarity NPD7834 Approved
0.598 Remote Similarity NPD8261 Discontinued
0.596 Remote Similarity NPD7981 Discontinued
0.5951 Remote Similarity NPD549 Approved
0.5951 Remote Similarity NPD1118 Discontinued
0.5949 Remote Similarity NPD3497 Clinical (unspecified phase)
0.5901 Remote Similarity NPD1121 Approved
0.5901 Remote Similarity NPD1120 Approved
0.5897 Remote Similarity NPD8629 Discontinued
0.5882 Remote Similarity NPD7980 Clinical (unspecified phase)
0.5862 Remote Similarity NPD276 Clinical (unspecified phase)
0.5857 Remote Similarity NPD8292 Phase 2
0.5856 Remote Similarity NPD1037 Clinical (unspecified phase)
0.5825 Remote Similarity NPD1249 Clinical (unspecified phase)
0.5813 Remote Similarity NPD545 Clinical (unspecified phase)
0.5813 Remote Similarity NPD547 Clinical (unspecified phase)
0.5801 Remote Similarity NPD3347 Clinical (unspecified phase)
0.5789 Remote Similarity NPD7842 Phase 2
0.5789 Remote Similarity NPD9606 Approved
0.5783 Remote Similarity NPD1117 Clinical (unspecified phase)
0.5759 Remote Similarity NPD870 Clinical (unspecified phase)
0.5752 Remote Similarity NPD9607 Approved
0.5752 Remote Similarity NPD307 Approved
0.5751 Remote Similarity NPD978 Clinical (unspecified phase)
0.575 Remote Similarity NPD8410 Clinical (unspecified phase)
0.5739 Remote Similarity NPD1335 Approved
0.5735 Remote Similarity NPD8075 Discontinued
0.5695 Remote Similarity NPD9374 Approved
0.5689 Remote Similarity NPD185 Approved
0.5686 Remote Similarity NPD9360 Approved
0.5684 Remote Similarity NPD7138 Phase 2
0.5673 Remote Similarity NPD8105 Discontinued
0.567 Remote Similarity NPD8113 Phase 2
0.5667 Remote Similarity NPD1777 Approved
0.5667 Remote Similarity NPD9373 Approved
0.5667 Remote Similarity NPD1776 Approved
0.5665 Remote Similarity NPD9605 Phase 3
0.5663 Remote Similarity NPD193 Suspended
0.566 Remote Similarity NPD1356 Approved
0.566 Remote Similarity NPD1354 Approved
0.566 Remote Similarity NPD1355 Clinical (unspecified phase)
0.5655 Remote Similarity NPD8837 Clinical (unspecified phase)
0.5648 Remote Similarity NPD994 Phase 2
0.5648 Remote Similarity NPD996 Phase 2
0.5644 Remote Similarity NPD1119 Phase 2
0.564 Remote Similarity NPD3085 Phase 1
0.5632 Remote Similarity NPD1369 Phase 2
0.5632 Remote Similarity NPD1030 Approved
0.5632 Remote Similarity NPD1029 Clinical (unspecified phase)
0.5632 Remote Similarity NPD1750 Clinical (unspecified phase)
0.5632 Remote Similarity NPD1027 Approved
0.5625 Remote Similarity NPD2624 Phase 2
0.5621 Remote Similarity NPD249 Approved
0.5621 Remote Similarity NPD1368 Approved
0.5621 Remote Similarity NPD250 Approved
0.5621 Remote Similarity NPD166 Approved
0.5619 Remote Similarity NPD460 Discontinued
0.5618 Remote Similarity NPD516 Clinical (unspecified phase)
0.5607 Remote Similarity NPD3086 Phase 3
0.56 Remote Similarity NPD9375 Discontinued

  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