NP-MRD: Showing NP-Card for Serylhistidine (NP0136628)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

1.0

Created at

2022-05-12 15:19:26 UTC

Updated at

2022-05-12 15:19:26 UTC

NP-MRD ID

NP0136628

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Serylhistidine

Description

Serylhistidine, also known as S-H or L-ser-L-his, belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. Serylhistidine is a very strong basic compound (based on its pKa). Serylhistidine is found in Trypanosoma brucei. It was first documented in 2000 (PMID: 10986393). It is an incomplete breakdown product of protein digestion or protein catabolism.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 31  0  0  0  0  0  0  0  0999 V2000
   -2.1565   -0.7578    1.8431 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7638   -0.3954    0.5887 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6220    0.8206    0.7103 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6499    0.6105    1.6263 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7914   -0.2356   -0.5031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2229    0.0793   -1.6351 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3846   -0.4230   -0.3295 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5075   -0.2480   -1.4502 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5323    0.8229   -1.2671 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4760    0.6242   -0.1555 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6795   -0.4417    0.6871 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6660   -0.1183    1.5700 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0733    1.1096    1.2953 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3765    1.5646    0.2727 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1106   -1.5412   -1.8799 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8869   -2.6462   -1.3655 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9986   -1.4912   -2.9504 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7514    0.0877    2.3332 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9297   -1.0875    2.4712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4397   -1.2505    0.3050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1244    0.9795   -0.2825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0536    1.7240    0.9861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4056    0.1402    1.2003 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0125   -0.6796    0.5897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1115    0.0751   -2.3443 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0120    1.8221   -1.1953 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1691    0.9200   -2.1987 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1877   -1.3894    0.6872 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0369   -0.7207    2.3249 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8469    1.7053    1.7876 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8345   -0.8587   -3.7216 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  2  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
  8 15  1  0
 15 17  1  0
 15 16  2  0
 14 10  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  6
  3 21  1  0
  3 22  1  0
  4 23  1  0
  7 24  1  0
  8 25  1  6
  9 26  1  0
  9 27  1  0
 11 28  1  0
 12 29  1  0
 13 30  1  0
 17 31  1  0
M  END


  Mrv1652304062014112D          

 17 17  0  0  0  0            999 V2000
 2500.6653 2500.6131    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 2500.6653 2499.7881    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2501.3860 2499.3888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2502.1004 2499.8003    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2501.3860 2498.5638    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 2500.6715 2498.1503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2499.9570 2498.5638    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2502.1004 2498.1503    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2499.9509 2501.0246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2501.3798 2501.0246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2502.0942 2500.6131    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2501.3798 2501.8496    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2498.5645 2501.1074    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2497.8971 2500.6224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2498.1520 2499.8378    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 2498.9770 2499.8378    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2499.2319 2500.6224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  1  0  0  0
  1  9  1  0  0  0  0
  1 10  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  5  3  1  1  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  7  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
 16 17  2  0  0  0  0
 13 14  2  0  0  0  0
 13 17  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
  9 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0136628

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H](CO)C(=O)N[C@@H](CC1=CNC=N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N4O4/c10-6(3-14)8(15)13-7(9(16)17)1-5-2-11-4-12-5/h2,4,6-7,14H,1,3,10H2,(H,11,12)(H,13,15)(H,16,17)/t6-,7-/m0/s1

> <INCHI_KEY>
YZMPDHTZJJCGEI-BQBZGAKWSA-N

> <FORMULA>
C9H14N4O4

> <MOLECULAR_WEIGHT>
242.235

> <EXACT_MASS>
242.101504947

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
22.79940821607855

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-[(2S)-2-amino-3-hydroxypropanamido]-3-(1H-imidazol-4-yl)propanoic acid

> <ALOGPS_LOGP>
-2.98

> <JCHEM_LOGP>
-4.864612242182938

> <ALOGPS_LOGS>
-1.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.705230703533733

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2368709060678342

> <JCHEM_PKA_STRONGEST_BASIC>
7.870652676556493

> <JCHEM_POLAR_SURFACE_AREA>
141.33

> <JCHEM_REFRACTIVITY>
56.334399999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.42e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-[(2S)-2-amino-3-hydroxypropanamido]-3-(1H-imidazol-4-yl)propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-APR-20         0                                  
HETATM    1  C   UNK     0    4667.9094667.811   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0    4667.9094666.271   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0    4669.2544665.526   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    4670.5874666.294   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    4669.2544663.986   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    4667.9204663.214   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0    4666.5864663.986   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0    4670.5874663.214   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0    4666.5754668.579   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    4669.2424668.579   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0    4670.5764667.811   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    4669.2424670.119   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0    4663.9874668.734   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0    4662.7414667.828   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0    4663.2174666.364   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0    4664.7574666.364   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    4665.2334667.828   0.000  0.00  0.00           C+0
CONECT    1    2    9   10                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5                                                            
CONECT    9    1   17                                                       
CONECT   10    1   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13   14   17                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   17   15                                                       
CONECT   17   16   13    9                                                  
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END

View in JSmol

Synonyms

Value	Source
L-Ser-L-his	ChEBI
S-H	ChEBI
SH	ChEBI
L-Seryl-L-histidine	HMDB
N-L-Seryl-L-histidine	HMDB
N-Serylhistidine	HMDB
S-H Dipeptide	HMDB
SH Dipeptide	HMDB
Ser-his	HMDB
Serine histidine dipeptide	HMDB
Serine-histidine dipeptide	HMDB
Serinyl-histidine	HMDB
Serinylhistidine	HMDB
Seryl-histidine	HMDB
Serylhistidine	ChEBI

Chemical Formula

C₉H₁₄N₄O₄

Average Mass

242.2350 Da

Monoisotopic Mass

242.10150 Da

IUPAC Name

(2S)-2-[(2S)-2-amino-3-hydroxypropanamido]-3-(1H-imidazol-4-yl)propanoic acid

Traditional Name

(2S)-2-[(2S)-2-amino-3-hydroxypropanamido]-3-(1H-imidazol-4-yl)propanoic acid

CAS Registry Number

Not Available

SMILES

N[C@@H](CO)C(=O)N[C@@H](CC1=CNC=N1)C(O)=O

InChI Identifier

InChI=1S/C9H14N4O4/c10-6(3-14)8(15)13-7(9(16)17)1-5-2-11-4-12-5/h2,4,6-7,14H,1,3,10H2,(H,11,12)(H,13,15)(H,16,17)/t6-,7-/m0/s1

InChI Key

YZMPDHTZJJCGEI-BQBZGAKWSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Trypanosoma brucei	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
Histidine or derivatives
N-acyl-alpha-amino acid
N-acyl-l-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Serine or derivatives
Alpha-amino acid or derivatives
Imidazolyl carboxylic acid derivative
Azole
Imidazole
Heteroaromatic compound
Amino acid or derivatives
Carboxamide group
Carboxylic acid salt
Amino acid
Secondary carboxylic acid amide
Organoheterocyclic compound
Carboxylic acid
Monocarboxylic acid or derivatives
Azacycle
Primary alcohol
Hydrocarbon derivative
Organonitrogen compound
Primary aliphatic amine
Amine
Organic oxide
Organooxygen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Organopnictogen compound
Primary amine
Alcohol
Organic zwitterion
Organic salt
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

dipeptide (CHEBI:73651 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-3	ALOGPS
logP	-4.9	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	3.24	ChemAxon
pKa (Strongest Basic)	7.87	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	141.33 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	56.33 m³·mol⁻¹	ChemAxon
Polarizability	22.8 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

External Links

HMDB ID

HMDB0029041

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

7016093

PDB ID

Not Available

ChEBI ID

73651

Good Scents ID

Not Available

References

General References

Schmiedl A, Breitling F, Winter CH, Queitsch I, Dubel S: Effects of unpaired cysteines on yield, solubility and activity of different recombinant antibody constructs expressed in E. coli. J Immunol Methods. 2000 Aug 28;242(1-2):101-14. doi: 10.1016/s0022-1759(00)00243-x. [PubMed:10986393 ]

Showing NP-Card for Serylhistidine (NP0136628)

MOL for NP0136628 (Serylhistidine)

3D MOL for NP0136628 (Serylhistidine)

3D SDF for NP0136628 (Serylhistidine)

3D-SDF for NP0136628 (Serylhistidine)

PDB for NP0136628 (Serylhistidine)

3D PDB for NP0136628 (Serylhistidine)

SMILES for NP0136628 (Serylhistidine)

INCHI for NP0136628 (Serylhistidine)

Structure for NP0136628 (Serylhistidine)

3D Structure for NP0136628 (Serylhistidine)