MiMeDB: Showing metabocard for D-histidine (MMDBc0055866)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:09:21 UTC

Update Date

2025-10-07 16:04:20 UTC

Metabolite ID

MMDBc0055866

Metabolite Identification

Common Name

D-histidine

Description

D-histidine is a non-proteinogenic amino acid belonging to the class of metabolites. Its chemical structure features a chiral center, distinguishing it from L-histidine, with implications for its biological activity. Recent studies have highlighted D-histidine's role in combating biofilm formation, particularly against pathogens such as Aggregatibacter actinomycetemcomitans and Pseudomonas aeruginosa (PMID:41020610 ). D-histidine has been shown to inhibit biofilm formation and disrupt established biofilms in a concentration-dependent manner, without adversely affecting bacterial growth (PMID:41020610 ). Additionally, it downregulates the expression of virulence factors by inhibiting quorum sensing-related genes (PMID:41020610 ). Notably, when combined with antibiotics like amoxicillin, minocycline, and metronidazole, D-histidine enhances biofilm eradication, allowing for lower dosages of these antibiotics (PMID:41020610 ). This synergistic effect positions D-histidine as a promising adjunctive therapeutic agent, addressing the growing challenge of antibiotic resistance and biofilm-associated antibiotic tolerance in periodontal treatments (PMID:41020610 ).

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.274   4.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.274   5.930   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.608   3.620   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       1.830  -0.290   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0      -1.608   6.700   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.060   6.700   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       1.060   5.160   0.000  0.00  0.00           H+0
CONECT    1    4    5                                                       
CONECT    2    4    8                                                       
CONECT    3    8    9                                                       
CONECT    4    1    2    9                                                  
CONECT    5    1    6    7   12                                             
CONECT    6    5   10   11                                                  
CONECT    7    5                                                            
CONECT    8    2    3                                                       
CONECT    9    3    4                                                       
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12    5                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

Synonyms

Value	Source
(R)-alpha-Amino-1H-imidazole-4-propionic acid	ChEBI
D-Histidin	ChEBI
DHI	ChEBI
(R)-a-Amino-1H-imidazole-4-propionate	Generator
(R)-a-Amino-1H-imidazole-4-propionic acid	Generator
(R)-alpha-Amino-1H-imidazole-4-propionate	Generator
(R)-Α-amino-1H-imidazole-4-propionate	Generator
(R)-Α-amino-1H-imidazole-4-propionic acid	Generator

Molecular Formula

C₆H₉N₃O₂

Average Mass

155.157

Monoisotopic Mass

155.069476542

IUPAC Name

(2R)-2-amino-3-(1H-imidazol-5-yl)propanoic acid

Traditional Name

d-histidine

CAS Registry Number

Not Available

SMILES

[H][C@@](N)(CC1=CN=CN1)C(O)=O

InChI Identifier

InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/t5-/m1/s1

InChI Key

HNDVDQJCIGZPNO-RXMQYKEDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Histidine and derivatives

Alternative Parents

Substituents

Histidine or derivatives
Alpha-amino acid
D-alpha-amino acid
Imidazolyl carboxylic acid derivative
Aralkylamine
Azole
Imidazole
Heteroaromatic compound
Amino acid
Carboxylic acid
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Primary amine
Primary aliphatic amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

D-alpha-amino acid (CHEBI:27947 )
histidine (CHEBI:27947 )
Other amino acids (C06419 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-3.6	ChemAxon
pKa (Strongest Acidic)	1.85	ChemAxon
pKa (Strongest Basic)	9.44	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	92 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	38.06 m³·mol⁻¹	ChemAxon
Polarizability	14.82 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	529.9
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	454.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	39.4
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	218.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	296.1
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	314.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	401.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	1001.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	846.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	198.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	676.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	202.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	34.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	429.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	724.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	119.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	371.9
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	628.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	567.2

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	D-histidine_TMS_1	C[Si](C)(C)OC(=O)[C@H](N)CC1=CN=C[NH]1	standard non polar	2025-10-24	1651.66
Gas Chromatography	D-histidine_TMS_2	C[Si](C)(C)N[C@H](CC1=CN=C[NH]1)C(=O)O	standard non polar	2025-10-24	2204.29
Gas Chromatography	D-histidine_TMS_3	C[Si](C)(C)N1C=NC=C1C[C@@H](N)C(=O)O	standard non polar	2025-10-24	1991.85
Gas Chromatography	D-histidine_TMS_4	C[Si](C)(C)N[C@H](CC1=CN=C[NH]1)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1804.43
Gas Chromatography	D-histidine_TMS_5	C[Si](C)(C)OC(=O)[C@H](N)CC1=CN=CN1[Si](C)(C)C	standard non polar	2025-10-24	1656.3
Gas Chromatography	D-histidine_TMS_6	C[Si](C)(C)N([C@H](CC1=CN=C[NH]1)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-24	2300.14
Gas Chromatography	D-histidine_TMS_7	C[Si](C)(C)N[C@H](CC1=CN=CN1[Si](C)(C)C)C(=O)O	standard non polar	2025-10-24	2640.25
Gas Chromatography	D-histidine_TMS_8	C[Si](C)(C)OC(=O)[C@@H](CC1=CN=C[NH]1)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	2211.43
Gas Chromatography	D-histidine_TMS_9	C[Si](C)(C)N[C@H](CC1=CN=CN1[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard non polar	2025-10-24	1624.7
Gas Chromatography	D-histidine_TMS_10	C[Si](C)(C)N([C@H](CC1=CN=CN1[Si](C)(C)C)C(=O)O)[Si](C)(C)C	standard non polar	2025-10-24	2703.86
Gas Chromatography	D-histidine_TMS_11	C[Si](C)(C)OC(=O)[C@@H](CC1=CN=CN1[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard non polar	2025-10-24	1598.23
Gas Chromatography	D-histidine_TMS_1	C[Si](C)(C)OC(=O)[C@H](N)CC1=CN=C[NH]1	standard polar	2025-10-24	1850.21
Gas Chromatography	D-histidine_TMS_2	C[Si](C)(C)N[C@H](CC1=CN=C[NH]1)C(=O)O	standard polar	2025-10-24	2169.59
Gas Chromatography	D-histidine_TMS_3	C[Si](C)(C)N1C=NC=C1C[C@@H](N)C(=O)O	standard polar	2025-10-24	1938.13
Gas Chromatography	D-histidine_TMS_4	C[Si](C)(C)N[C@H](CC1=CN=C[NH]1)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	1948.57
Gas Chromatography	D-histidine_TMS_5	C[Si](C)(C)OC(=O)[C@H](N)CC1=CN=CN1[Si](C)(C)C	standard polar	2025-10-24	2095.22
Gas Chromatography	D-histidine_TMS_6	C[Si](C)(C)N([C@H](CC1=CN=C[NH]1)C(=O)O)[Si](C)(C)C	standard polar	2025-10-24	2165.62
Gas Chromatography	D-histidine_TMS_7	C[Si](C)(C)N[C@H](CC1=CN=CN1[Si](C)(C)C)C(=O)O	standard polar	2025-10-24	1708.75
Gas Chromatography	D-histidine_TMS_8	C[Si](C)(C)OC(=O)[C@@H](CC1=CN=C[NH]1)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	2089.78
Gas Chromatography	D-histidine_TMS_9	C[Si](C)(C)N[C@H](CC1=CN=CN1[Si](C)(C)C)C(=O)O[Si](C)(C)C	standard polar	2025-10-24	2628.21
Gas Chromatography	D-histidine_TMS_10	C[Si](C)(C)N([C@H](CC1=CN=CN1[Si](C)(C)C)C(=O)O)[Si](C)(C)C	standard polar	2025-10-24	1763.54
Gas Chromatography	D-histidine_TMS_11	C[Si](C)(C)OC(=O)[C@@H](CC1=CN=CN1[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C	standard polar	2025-10-24	1483.85

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Firmicutes	2	Human ; Human feces
Bacteria/Eubacteria	Proteobacteria	2	Human ; Human feces
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

64237

KEGG Compound ID

C06419

BioCyc ID

CPD-12151

BiGG ID

Not Available

Wikipedia Link

Histidine

METLIN ID

Not Available

PubChem Compound

71083

PDB ID

Not Available

ChEBI ID

27947

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for D-histidine (MMDBc0055866)

MOL for #<Metabolite:0x00005624c9dad1f0>

3D MOL for #<Metabolite:0x00005624c9dad1f0>

3D SDF for #<Metabolite:0x00005624c9dad1f0>

3D-SDF for #<Metabolite:0x00005624c9dad1f0>

PDB for #<Metabolite:0x00005624c9dad1f0>

3D PDB for #<Metabolite:0x00005624c9dad1f0>

SMILES for #<Metabolite:0x00005624c9dad1f0>

INCHI for #<Metabolite:0x00005624c9dad1f0>

Structure for #<Metabolite:0x00005624c9dad1f0>

3D Structure for #<Metabolite:0x00005624c9dad1f0>