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Showing NP-Card for D-Histidine (NP0351322)

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Record Information
Version2.0
Created at2025-07-16 23:01:58 UTC
Updated at2025-07-18 00:04:12 UTC
NP-MRD IDNP0351322
Natural Product DOIhttps://doi.org/10.57994/4343
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Histidine
DescriptionD-Histidine, also known as DHI, 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. D-Histidine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. D-Histidine was first documented in 2023 (PMID: 37992272). Based on a literature review a significant number of articles have been published on D-Histidine (PMID: 40549064) (PMID: 40195913) (PMID: 40126891) (PMID: 39918700) (PMID: 39832874) (PMID: 39728789).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0351322 (D-Histidine)


  Mrv2104 01202316122D          

 11 11  0  0  1  0            999 V2000
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1467    3.1768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8612    3.5893    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    3.5893    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8612    1.9393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  1  5  1  0  0  0  0
  2  6  1  0  0  0  0
  7  6  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  7 11  1  1  0  0  0
M  END
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3D MOL for NP0351322 (D-Histidine)

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3D SDF for NP0351322 (D-Histidine)

  Mrv2104 01202316122D          

 11 11  0  0  1  0            999 V2000
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1467    3.1768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8612    3.5893    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    3.5893    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8612    1.9393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  1  5  1  0  0  0  0
  2  6  1  0  0  0  0
  7  6  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  7 11  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0351322

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@H](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

> <FORMULA>
C6H9N3O2

> <MOLECULAR_WEIGHT>
155.157

> <EXACT_MASS>
155.069476542

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
14.815387729319788

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-3.6160224799542067

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.941172308417478

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.849972676704367

> <JCHEM_PKA_STRONGEST_BASIC>
9.437137464922305

> <JCHEM_POLAR_SURFACE_AREA>
92.0

> <JCHEM_REFRACTIVITY>
38.059000000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
d-histidine

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0351322 (D-Histidine)
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PDB for NP0351322 (D-Histidine)
HEADER    PROTEIN                                 20-JAN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JAN-23         0                                  
HETATM    1  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.306   1.175   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.290  -0.290   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.274   4.390   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.274   5.930   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.608   6.700   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.060   6.700   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0      -1.608   3.620   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
CONECT    6    2    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    7                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

Download
3D PDB for NP0351322 (D-Histidine)
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SMILES for NP0351322 (D-Histidine)
N[C@H](CC1=CN=CN1)C(O)=O
Download
INCHI for NP0351322 (D-Histidine)
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
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View in JSmol
Synonyms
ValueSource
(R)-alpha-Amino-1H-imidazole-4-propionic acidChEBI
D-HistidinChEBI
DHIChEBI
(R)-a-Amino-1H-imidazole-4-propionateGenerator
(R)-a-Amino-1H-imidazole-4-propionic acidGenerator
(R)-alpha-Amino-1H-imidazole-4-propionateGenerator
(R)-Α-amino-1H-imidazole-4-propionateGenerator
(R)-Α-amino-1H-imidazole-4-propionic acidGenerator
Chemical FormulaC6H9N3O2
Average Mass155.1570 Da
Monoisotopic Mass155.06948 Da
IUPAC Name(2R)-2-amino-3-(1H-imidazol-5-yl)propanoic acid
Traditional Named-histidine
CAS Registry NumberNot Available
SMILES
N[C@H](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 KeyHNDVDQJCIGZPNO-RXMQYKEDSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
HMBC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
HSQC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
COSY NMR[1H, 1H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
1D NMR1H NMR Spectrum (1D, 600.0 MHz, C2D6OS, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600.0, C2D6OS, simulated)rjm4kd@umsystem.eduSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
Species
Species of OriginNot Available
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.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentHistidine 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 FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-3.6ChemAxon
pKa (Strongest Acidic)1.85ChemAxon
pKa (Strongest Basic)9.44ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area92 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity38.06 m³·mol⁻¹ChemAxon
Polarizability14.82 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC06419  
BioCyc IDCPD-12151  
BiGG IDNot Available
Wikipedia LinkHistidine  
METLIN IDNot Available
PubChem Compound71083  
PDB IDNot Available
ChEBI ID27947  
Good Scents IDNot Available
References
General References
  1. Nakanishi R, Fujihara A: D-Amino acid analysis in solution using the photochemical properties of protonated adenosine. Photochem Photobiol Sci. 2025 Jul;24(7):1153-1158. doi:  10.1007/s43630-025-00751-6. Epub 2025 Jun 23. [PubMed:40549064  ] 
  2. Sarkar S, Mathath AV, Chakraborty D: Controlling the Morphology and Orientation of the Helical Self-Assembly of Pyrazine Derivatives by Tuning Hydration Shells. Chemphyschem. 2025 Jun 23;26(12):e202400951. doi: 10.1002/cphc.202400951. Epub  2025 May 7. [PubMed:40195913  ] 
  3. Chen M, Gao L, Liu H, Yu J, Zhao F, Bai L, Chu H, Zhao M, Qin S: Separation of dithiothreitol and dithioerythritol by an open tubular capillary electrochromatographic column with an MOF modified by histidine as the stationary phase. Anal Methods. 2025 Apr 3;17(14):2887-2893. doi: 10.1039/d5ay00097a. [PubMed:40126891  ] 
  4. Huang W, Chen X, Xu X, Pan S: Urinary metabolomics analysis of patients with renal tubular dysfunction after PCI surgery. Int Urol Nephrol. 2025 Jul;57(7):2237-2244. doi: 10.1007/s11255-025-04397-2. Epub  2025 Feb 7. [PubMed:39918700  ] 
  5. Gao X, Bai R, Yang J, Luo S, Yuan H, Wang L, Fu Z: D-Histidine modulated chiral metal-organic frameworks for discriminating 3,4-Dihydroxyphenylalanine enantiomers based on a chemiluminescence quenching mode. Anal Chim Acta. 2025 Feb 15;1339:343606. doi: 10.1016/j.aca.2024.343606. Epub  2025 Jan 1. [PubMed:39832874  ] 
  6. Bendejacq-Seychelles A, Martinez L, Correard A, Totozafy JC, Steinberg C, Pouvreau JB, Reibel C, Mouille G, Mondy S, Poulin L, Gibot-Leclerc S: Image Analysis and Untargeted Metabolomics Reveal Potential Phytotoxins from Fusarium venenatum Against Major Parasitic Weed Phelipanche ramosa (L.) Pomel. Toxins (Basel). 2024 Dec 10;16(12):531. doi: 10.3390/toxins16120531. [PubMed:39728789  ] 
  7. Xu M, Vallieres C, Finnis C, Winzer K, Avery SV: Exploiting phenotypic heterogeneity to improve production of glutathione by yeast. Microb Cell Fact. 2024 Oct 7;23(1):267. doi: 10.1186/s12934-024-02536-5. [PubMed:39375675  ] 
  8. Li T, Li H, Chen J, Yu Y, Chen S, Wang J, Qiu H: Histidine-modified pillar[5]arene-functionalized mesoporous silica materials for highly selective enantioseparation. J Chromatogr A. 2024 Jul 19;1727:465011. doi: 10.1016/j.chroma.2024.465011. Epub  2024 May 18. [PubMed:38776604  ] 
  9. Sun Q, Bao B, Dong W, Lyu Y, Wang M, Xi Z, Han J, Guo R: Expression of chiral molecular and supramolecular structure on enantioselective catalytic activity. J Colloid Interface Sci. 2024 Sep;669:944-951. doi: 10.1016/j.jcis.2024.05.027.  Epub 2024 May 9. [PubMed:38759593  ] 
  10. Qin S, Meng F, Jin F, Xu X, Zhao M, Chu H, Gao L, Liu S: Dual-functional porphyrinic zirconium-based metal-organic framework for the fluorescent sensing of histidine enantiomers and Hg(2). Anal Methods. 2024 Apr 18;16(15):2386-2399. doi: 10.1039/d3ay02241b. [PubMed:38572640  ] 
  11. Zhang H, Mi Z, Wang J, Zhang J: D-histidine combated biofilm formation and enhanced the effect of amikacin against Pseudomonas aeruginosa in vitro. Arch Microbiol. 2024 Mar 11;206(4):148. doi: 10.1007/s00203-024-03918-4. [PubMed:38462558  ] 
  12. Beyranvand F, Khosravi A, Zabihi F, Nemati M, Gholami MF, Tavakol M, Beyranvand S, Satari S, Rabe JP, Salimi A, Cheng C, Adeli M: Synthesis of Chiral Triazine Frameworks for Enantiodiscrimination. ACS Appl Mater Interfaces. 2023 Dec 6;15(48):56213-56222. doi:  10.1021/acsami.3c16659. Epub 2023 Nov 22. [PubMed:37992272  ]