Structure

Physi-Chem Properties

Molecular Weight:  163.05
Volume:  144.711
LogP:  -2.588
LogD:  -1.977
LogS:  -0.151
# Rotatable Bonds:  4
TPSA:  120.85
# H-Bond Aceptor:  6
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.272
Synthetic Accessibility Score:  3.483
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.241
MDCK Permeability:  0.00803602859377861
Pgp-inhibitor:  0.001
Pgp-substrate:  0.049
Human Intestinal Absorption (HIA):  0.831
20% Bioavailability (F20%):  0.9
30% Bioavailability (F30%):  0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.524
Plasma Protein Binding (PPB):  15.250015258789062%
Volume Distribution (VD):  0.419
Pgp-substrate:  83.53297424316406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.03
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.05
CYP2C9-inhibitor:  0.036
CYP2C9-substrate:  0.126
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.162
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.026

ADMET: Excretion

Clearance (CL):  2.51
Half-life (T1/2):  0.852

ADMET: Toxicity

hERG Blockers:  0.034
Human Hepatotoxicity (H-HT):  0.263
Drug-inuced Liver Injury (DILI):  0.065
AMES Toxicity:  0.027
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.006
Skin Sensitization:  0.205
Carcinogencity:  0.017
Eye Corrosion:  0.003
Eye Irritation:  0.07
Respiratory Toxicity:  0.273

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

  Natural Product: NPC88898

Natural Product ID:  NPC88898
Common Name*:   (2S,4S)-4-Hydroxyglutamic Acid
IUPAC Name:   (2S,4S)-2-amino-4-hydroxypentanedioic acid
Synonyms:   (2S,4S)-4-Hydroxyglutamic Acid
Standard InCHIKey:  HBDWQSHEVMSFGY-HRFVKAFMSA-N
Standard InCHI:  InChI=1S/C5H9NO5/c6-2(4(8)9)1-3(7)5(10)11/h2-3,7H,1,6H2,(H,8,9)(H,10,11)/t2-,3-/m0/s1
SMILES:  C([C@@H](C(=O)O)N)[C@@H](C(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL197110
PubChem CID:   192790
44286641
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
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.lwt.2014.11.023]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae 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
NPT3080 Individual Protein Metabotropic glutamate receptor 1 Rattus norvegicus EC50 = 11000.0 nM PMID[546147]
NPT3081 Individual Protein Metabotropic glutamate receptor 2 Rattus norvegicus EC50 = 137000.0 nM PMID[546147]
NPT4028 Individual Protein Metabotropic glutamate receptor 8 Rattus norvegicus EC50 = 53000.0 nM PMID[546147]
NPT3080 Individual Protein Metabotropic glutamate receptor 1 Rattus norvegicus Rmax = 95.0 mM PMID[546147]
NPT3081 Individual Protein Metabotropic glutamate receptor 2 Rattus norvegicus Rmax = 60.0 mM PMID[546147]
NPT4028 Individual Protein Metabotropic glutamate receptor 8 Rattus norvegicus Rmax = 94.0 mM PMID[546147]
NPT1520 Individual Protein Excitatory amino acid transporter 1 Homo sapiens Km = 140000.0 nM PMID[546148]
NPT1520 Individual Protein Excitatory amino acid transporter 1 Homo sapiens pKm = 4.06 n.a. PMID[546148]
NPT1519 Individual Protein Excitatory amino acid transporter 2 Homo sapiens Km = 67000.0 nM PMID[546148]
NPT1519 Individual Protein Excitatory amino acid transporter 2 Homo sapiens pKm = 4.21 n.a. PMID[546148]
NPT1518 Individual Protein Excitatory amino acid transporter 3 Homo sapiens Km = 81000.0 nM PMID[546148]
NPT1518 Individual Protein Excitatory amino acid transporter 3 Homo sapiens pKm = 4.16 n.a. PMID[546148]

☑ 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 NPC88898 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 NPC106216
0.7931 Intermediate Similarity NPC137958
0.7931 Intermediate Similarity NPC273330
0.7705 Intermediate Similarity NPC2801
0.7619 Intermediate Similarity NPC327895
0.7619 Intermediate Similarity NPC93861
0.7619 Intermediate Similarity NPC190385
0.7619 Intermediate Similarity NPC112224
0.7619 Intermediate Similarity NPC43169
0.7385 Intermediate Similarity NPC68974
0.7069 Intermediate Similarity NPC38891
0.7069 Intermediate Similarity NPC242655
0.6923 Remote Similarity NPC219340
0.6866 Remote Similarity NPC143722
0.6833 Remote Similarity NPC136159
0.6825 Remote Similarity NPC197087
0.6825 Remote Similarity NPC190184
0.678 Remote Similarity NPC327698
0.678 Remote Similarity NPC118459
0.6769 Remote Similarity NPC325985
0.6761 Remote Similarity NPC196359
0.6761 Remote Similarity NPC78312
0.6761 Remote Similarity NPC135539
0.6761 Remote Similarity NPC221764
0.6761 Remote Similarity NPC118524
0.6721 Remote Similarity NPC327542
0.6667 Remote Similarity NPC107224
0.6613 Remote Similarity NPC93888
0.6613 Remote Similarity NPC270805
0.6562 Remote Similarity NPC263065
0.6562 Remote Similarity NPC189178
0.6517 Remote Similarity NPC160066
0.6515 Remote Similarity NPC38463
0.65 Remote Similarity NPC208793
0.65 Remote Similarity NPC285322
0.65 Remote Similarity NPC329263
0.6479 Remote Similarity NPC50047
0.6471 Remote Similarity NPC321536
0.6452 Remote Similarity NPC93081
0.6452 Remote Similarity NPC140872
0.6429 Remote Similarity NPC327252
0.6389 Remote Similarity NPC325534
0.6364 Remote Similarity NPC322573
0.6349 Remote Similarity NPC226027
0.6349 Remote Similarity NPC162620
0.6349 Remote Similarity NPC62045
0.6349 Remote Similarity NPC174246
0.6349 Remote Similarity NPC316231
0.6349 Remote Similarity NPC112890
0.6349 Remote Similarity NPC43204
0.6349 Remote Similarity NPC84636
0.6349 Remote Similarity NPC245027
0.6349 Remote Similarity NPC324825
0.6316 Remote Similarity NPC185084
0.6301 Remote Similarity NPC222327
0.6301 Remote Similarity NPC188231
0.6265 Remote Similarity NPC320936
0.6212 Remote Similarity NPC322091
0.6212 Remote Similarity NPC279661
0.6212 Remote Similarity NPC183845
0.6212 Remote Similarity NPC60672
0.6212 Remote Similarity NPC19676
0.6212 Remote Similarity NPC323401
0.619 Remote Similarity NPC153370
0.6129 Remote Similarity NPC309658
0.6119 Remote Similarity NPC6883
0.6111 Remote Similarity NPC289691
0.6102 Remote Similarity NPC121517
0.6102 Remote Similarity NPC168375
0.6102 Remote Similarity NPC326992
0.6098 Remote Similarity NPC314466
0.6061 Remote Similarity NPC277878
0.6034 Remote Similarity NPC18188
0.6032 Remote Similarity NPC101249
0.6027 Remote Similarity NPC325597
0.6027 Remote Similarity NPC472609
0.6027 Remote Similarity NPC174304
0.6027 Remote Similarity NPC160661
0.5972 Remote Similarity NPC2432
0.5972 Remote Similarity NPC69669
0.5972 Remote Similarity NPC22774
0.5972 Remote Similarity NPC306462
0.5972 Remote Similarity NPC150680
0.5972 Remote Similarity NPC218150
0.597 Remote Similarity NPC196612
0.5902 Remote Similarity NPC291186
0.5902 Remote Similarity NPC276294
0.5902 Remote Similarity NPC167986
0.5882 Remote Similarity NPC327831
0.5867 Remote Similarity NPC322801
0.5867 Remote Similarity NPC129100
0.5867 Remote Similarity NPC291650
0.5833 Remote Similarity NPC66043
0.5811 Remote Similarity NPC471780
0.5811 Remote Similarity NPC75435
0.5811 Remote Similarity NPC223386
0.5811 Remote Similarity NPC142290
0.5811 Remote Similarity NPC471892
0.5811 Remote Similarity NPC198341
0.5806 Remote Similarity NPC323974
0.5806 Remote Similarity NPC325097
0.5806 Remote Similarity NPC132307
0.5806 Remote Similarity NPC126925
0.5789 Remote Similarity NPC319046
0.5775 Remote Similarity NPC290106
0.5775 Remote Similarity NPC193593
0.5775 Remote Similarity NPC143809
0.5775 Remote Similarity NPC76726
0.5747 Remote Similarity NPC469363
0.5738 Remote Similarity NPC35661
0.5738 Remote Similarity NPC226265
0.5738 Remote Similarity NPC219143
0.5733 Remote Similarity NPC286851
0.5733 Remote Similarity NPC303798
0.5733 Remote Similarity NPC315980
0.5714 Remote Similarity NPC311668
0.5714 Remote Similarity NPC278209
0.5714 Remote Similarity NPC126779
0.5714 Remote Similarity NPC270088
0.5714 Remote Similarity NPC10262
0.5714 Remote Similarity NPC65832
0.5714 Remote Similarity NPC8979
0.5696 Remote Similarity NPC55274
0.5692 Remote Similarity NPC247546
0.5692 Remote Similarity NPC172086
0.5672 Remote Similarity NPC19576
0.5672 Remote Similarity NPC200550
0.5672 Remote Similarity NPC29950
0.5672 Remote Similarity NPC155156
0.5667 Remote Similarity NPC477729
0.5645 Remote Similarity NPC313565
0.5645 Remote Similarity NPC228782
0.5645 Remote Similarity NPC259982
0.5634 Remote Similarity NPC302003
0.5634 Remote Similarity NPC293692
0.5634 Remote Similarity NPC220922
0.5634 Remote Similarity NPC204709
0.5634 Remote Similarity NPC11433
0.5634 Remote Similarity NPC245346
0.5634 Remote Similarity NPC189301
0.5634 Remote Similarity NPC176164
0.5625 Remote Similarity NPC136476
0.5625 Remote Similarity NPC476248
0.5625 Remote Similarity NPC49952
0.5616 Remote Similarity NPC62507
0.5616 Remote Similarity NPC8087
0.5606 Remote Similarity NPC293378
0.5606 Remote Similarity NPC46254

  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 NPC88898 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
0.7931 Intermediate Similarity NPD8871 Approved
0.7931 Intermediate Similarity NPD8872 Phase 3
0.7667 Intermediate Similarity NPD8851 Phase 1
0.7619 Intermediate Similarity NPD9023 Clinical (unspecified phase)
0.6825 Remote Similarity NPD8785 Approved
0.6761 Remote Similarity NPD8868 Approved
0.6761 Remote Similarity NPD1429 Clinical (unspecified phase)
0.6613 Remote Similarity NPD8624 Approved
0.6567 Remote Similarity NPD9433 Approved
0.6562 Remote Similarity NPD9204 Approved
0.6562 Remote Similarity NPD9205 Approved
0.6522 Remote Similarity NPD574 Approved
0.65 Remote Similarity NPD8610 Approved
0.6452 Remote Similarity NPD8809 Approved
0.6452 Remote Similarity NPD8808 Approved
0.6429 Remote Similarity NPD575 Clinical (unspecified phase)
0.6389 Remote Similarity NPD8952 Approved
0.6349 Remote Similarity NPD9017 Approved
0.6349 Remote Similarity NPD9018 Approved
0.6349 Remote Similarity NPD9016 Clinical (unspecified phase)
0.6349 Remote Similarity NPD9044 Approved
0.6301 Remote Similarity NPD9421 Phase 1
0.619 Remote Similarity NPD8614 Approved
0.6118 Remote Similarity NPD619 Phase 3
0.6061 Remote Similarity NPD65 Approved
0.6061 Remote Similarity NPD66 Approved
0.6061 Remote Similarity NPD64 Approved
0.6061 Remote Similarity NPD9009 Approved
0.6061 Remote Similarity NPD9008 Approved
0.6061 Remote Similarity NPD9007 Approved
0.6061 Remote Similarity NPD72 Approved
0.6061 Remote Similarity NPD9010 Approved
0.6061 Remote Similarity NPD9011 Approved
0.6061 Remote Similarity NPD8960 Approved
0.6034 Remote Similarity NPD8623 Phase 1
0.6032 Remote Similarity NPD8866 Approved
0.6032 Remote Similarity NPD8867 Approved
0.6027 Remote Similarity NPD348 Approved
0.6 Remote Similarity NPD8609 Approved
0.5974 Remote Similarity NPD9446 Approved
0.5972 Remote Similarity NPD9028 Phase 2
0.5972 Remote Similarity NPD9026 Phase 2
0.5972 Remote Similarity NPD9029 Phase 3
0.5972 Remote Similarity NPD9027 Phase 3
0.5926 Remote Similarity NPD3160 Suspended
0.5914 Remote Similarity NPD881 Approved
0.5902 Remote Similarity NPD8805 Approved
0.5902 Remote Similarity NPD8804 Approved
0.5882 Remote Similarity NPD8971 Approved
0.5875 Remote Similarity NPD376 Approved
0.5875 Remote Similarity NPD11 Approved
0.5867 Remote Similarity NPD9032 Approved
0.5867 Remote Similarity NPD9033 Approved
0.5867 Remote Similarity NPD9030 Approved
0.5867 Remote Similarity NPD9031 Approved
0.5867 Remote Similarity NPD886 Clinical (unspecified phase)
0.5823 Remote Similarity NPD9109 Discontinued
0.5806 Remote Similarity NPD8798 Approved
0.5806 Remote Similarity NPD9019 Approved
0.5789 Remote Similarity NPD337 Discontinued
0.5789 Remote Similarity NPD4241 Registered
0.5738 Remote Similarity NPD8217 Clinical (unspecified phase)
0.5738 Remote Similarity NPD8216 Approved
0.5714 Remote Similarity NPD4242 Approved
0.5714 Remote Similarity NPD73 Approved
0.5694 Remote Similarity NPD9239 Approved
0.5694 Remote Similarity NPD9240 Approved
0.5692 Remote Similarity NPD9005 Phase 3
0.5692 Remote Similarity NPD9003 Clinical (unspecified phase)
0.5692 Remote Similarity NPD9004 Approved
0.5676 Remote Similarity NPD1151 Approved
0.5672 Remote Similarity NPD8847 Approved
0.5672 Remote Similarity NPD8846 Approved
0.5672 Remote Similarity NPD61 Approved
0.5667 Remote Similarity NPD3716 Discontinued
0.5658 Remote Similarity NPD8842 Clinical (unspecified phase)
0.5638 Remote Similarity NPD6428 Approved
0.5634 Remote Similarity NPD8959 Approved
0.5634 Remote Similarity NPD8865 Approved
0.5606 Remote Similarity NPD71 Approved
0.5606 Remote Similarity NPD9126 Approved
0.5606 Remote Similarity NPD9129 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