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Showing NP-Card for cis-4-hydroxy-d-proline (NP0213696)

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Record Information
Version1.0
Created at2022-09-05 12:45:26 UTC
Updated at2022-09-05 12:45:26 UTC
NP-MRD IDNP0213696
Secondary Accession NumbersNone
Natural Product Identification
Common Namecis-4-hydroxy-d-proline
DescriptionCis-4-Hydroxy-D-proline belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Cis-4-Hydroxy-D-proline is a very strong basic compound (based on its pKa). Cis-4-Hydroxy-D-proline exists in all living organisms, ranging from bacteria to humans. cis-4-hydroxy-d-proline is found in Daphnia pulex and Mus musculus. It was first documented in 2011 (PMID: 21447597). A 4-hydroxy-D-proline in which the hydroxy group at position 4 has R-configuration (PMID: 22770225).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0213696 (cis-4-hydroxy-d-proline)


  Mrv0541 05161318222D          

  9  9  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -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  2  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1296   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  4  5  1  6  0  0  0
  6  2  1  0  0  0  0
  6  4  1  0  0  0  0
  3  7  1  6  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
M  END
Download

3D MOL for NP0213696 (cis-4-hydroxy-d-proline)

     RDKit          3D

 18 18  0  0  0  0  0  0  0  0999 V2000
    1.6322    1.9095   -0.6000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6892    0.9101   -0.0171 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9038    0.1890    0.1439 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5432    0.2267    0.7249 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7295    0.9438    0.1456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4609   -0.1068   -0.6674 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7938   -0.1971   -1.8975 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0913   -1.3522    0.1537 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2941   -1.0839    0.2302 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2025   -0.2068    0.9789 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6225    0.4123    1.7647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4710    1.8116   -0.4592 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3712    1.2416    0.9753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5328    0.0448   -0.7599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3571    0.6696   -2.1239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2613   -2.2652   -0.4437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6681   -1.3258    1.0848 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8495   -1.8212    0.7668 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  8  1  0
  8  9  1  0
  9  4  1  0
  4  5  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  5  6  1  0
  7 15  1  0
  6 14  1  6
  8 16  1  0
  8 17  1  0
  9 18  1  0
  4 11  1  1
  5 12  1  0
  5 13  1  0
  3 10  1  0
M  END
Download

3D SDF for NP0213696 (cis-4-hydroxy-d-proline)


  Mrv0541 05161318222D          

  9  9  0  0  0  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -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  2  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1296   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  4  5  1  6  0  0  0
  6  2  1  0  0  0  0
  6  4  1  0  0  0  0
  3  7  1  6  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0213696

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1CN[C@H](C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO3/c7-3-1-4(5(8)9)6-2-3/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4-/m1/s1

> <INCHI_KEY>
PMMYEEVYMWASQN-QWWZWVQMSA-N

> <FORMULA>
C5H9NO3

> <MOLECULAR_WEIGHT>
131.1299

> <EXACT_MASS>
131.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
12.340473752746178

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,4R)-4-hydroxypyrrolidine-2-carboxylic acid

> <ALOGPS_LOGP>
-3.31

> <JCHEM_LOGP>
-3.7163188466782064

> <ALOGPS_LOGS>
0.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.856641323999913

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.641381950764853

> <JCHEM_PKA_STRONGEST_BASIC>
10.617096890348787

> <JCHEM_POLAR_SURFACE_AREA>
69.56

> <JCHEM_REFRACTIVITY>
29.3822

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.92e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cis-4-hydroxy-D-proline

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0213696 (cis-4-hydroxy-d-proline)

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PDB for NP0213696 (cis-4-hydroxy-d-proline)
HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.735  -1.536   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.290  -0.290   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.267  -1.375   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       2.109  -2.943   0.000  0.00  0.00           O+0
CONECT    1    3    4                                                       
CONECT    2    3    6                                                       
CONECT    3    1    2    7                                                  
CONECT    4    1    5    6                                                  
CONECT    5    4    8    9                                                  
CONECT    6    2    4                                                       
CONECT    7    3                                                            
CONECT    8    5                                                            
CONECT    9    5                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0213696 (cis-4-hydroxy-d-proline)
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SMILES for NP0213696 (cis-4-hydroxy-d-proline)
O[C@H]1CN[C@H](C1)C(O)=O
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INCHI for NP0213696 (cis-4-hydroxy-d-proline)
InChI=1S/C5H9NO3/c7-3-1-4(5(8)9)6-2-3/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC5H9NO3
Average Mass131.1299 Da
Monoisotopic Mass131.05824 Da
IUPAC Name(2R,4R)-4-hydroxypyrrolidine-2-carboxylic acid
Traditional Namecis-4-hydroxy-D-proline
CAS Registry NumberNot Available
SMILES
O[C@H]1CN[C@H](C1)C(O)=O
InChI Identifier
InChI=1S/C5H9NO3/c7-3-1-4(5(8)9)6-2-3/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4-/m1/s1
InChI KeyPMMYEEVYMWASQN-QWWZWVQMSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Daphnia pulexLOTUS Database
Mus musculusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline 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 ParentProline and derivatives  
Alternative Parents
Substituents
  • Proline or derivatives
    • 

  • Alpha-amino acid
    • 

  • D-alpha-amino acid
    • 

  • Pyrrolidine carboxylic acid
    • 

  • Pyrrolidine carboxylic acid or derivatives
    • 

  • Pyrrolidine
    • 

  • 1,2-aminoalcohol
    • 

  • Amino acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Secondary aliphatic amine
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Azacycle
    • 

  • Secondary amine
    • 

  • Organoheterocyclic compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Alcohol
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Carbonyl group
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic 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-3.3ALOGPS
logP-3.7ChemAxon
logS0.57ALOGPS
pKa (Strongest Acidic)1.64ChemAxon
pKa (Strongest Basic)10.62ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.56 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.38 m³·mol⁻¹ChemAxon
Polarizability12.34 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0060460  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC03440  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440014  
PDB IDNot Available
ChEBI ID16231  
Good Scents IDNot Available
References
General References
  1. Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C: Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem. 2012 Aug 7;84(15):6429-37. doi: 10.1021/ac300829f. Epub 2012 Jul 17. [PubMed:22770225  ] 
  2. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597  ] 
  3. LOTUS database [Link]