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Showing NP-Card for 3-Hydroxy-L-proline (NP0136741)

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Record Information
Version1.0
Created at2022-05-12 15:22:19 UTC
Updated at2022-05-12 15:22:19 UTC
NP-MRD IDNP0136741
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Hydroxy-L-proline
Description3-Hydroxy-L-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. 3-Hydroxy-L-proline is found in Brachystegia longifolia. It was first documented in 2014 (PMID: 24980702). 3-Hydroxy-L-proline is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0136741 (3-Hydroxy-L-proline)


  Mrv1652304202019292D          

  9  9  0  0  1  0            999 V2000
   -1.0157    0.9637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8757    0.1507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5097   -0.3771    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1015   -0.1345    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1228   -0.9285    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9471   -0.9605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2323   -0.1864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5842    0.3241    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6162    1.1485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  2  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  1  1  0  0  0
M  END
Download

3D MOL for NP0136741 (3-Hydroxy-L-proline)

     RDKit          3D

 18 18  0  0  0  0  0  0  0  0999 V2000
    2.0869    1.6210   -0.2644 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8890    0.4624    0.0329 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9337   -0.4996   -0.0760 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5464   -0.0516    0.5468 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1993   -1.2671   -0.2045 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2319   -1.3060    0.1774 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6159    0.0366   -0.4058 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5573    0.9267    0.1843 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1338    1.9117   -0.7226 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4800   -0.4831   -0.8952 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6563   -0.2383    1.6024 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6691   -2.0683    0.2754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2528   -1.2358    1.2550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7331   -2.1411   -0.2573 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4989   -0.0054   -1.5113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5990    0.3745   -0.1095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9591    1.3704    1.0995 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8789    2.5930   -0.7271 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  4  8  1  0
  9 18  1  0
  8 17  1  1
  7 15  1  0
  7 16  1  0
  6 13  1  0
  6 14  1  0
  5 12  1  0
  4 11  1  1
  3 10  1  0
M  END
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3D SDF for NP0136741 (3-Hydroxy-L-proline)


  Mrv1652304202019292D          

  9  9  0  0  1  0            999 V2000
   -1.0157    0.9637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8757    0.1507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5097   -0.3771    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1015   -0.1345    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1228   -0.9285    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9471   -0.9605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2323   -0.1864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5842    0.3241    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6162    1.1485    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  4  2  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0136741

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO3/c7-3-1-2-6-4(3)5(8)9/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4+/m0/s1

> <INCHI_KEY>
BJBUEDPLEOHJGE-IUYQGCFVSA-N

> <FORMULA>
C5H9NO3

> <MOLECULAR_WEIGHT>
131.1299

> <EXACT_MASS>
131.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.26841822441352

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S)-3-hydroxypyrrolidine-2-carboxylic acid

> <ALOGPS_LOGP>
-3.18

> <JCHEM_LOGP>
-3.716320522797164

> <ALOGPS_LOGS>
0.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.58501555709157

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6109755599539857

> <JCHEM_PKA_STRONGEST_BASIC>
10.616535665776542

> <JCHEM_POLAR_SURFACE_AREA>
69.56

> <JCHEM_REFRACTIVITY>
29.3822

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.31e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-L-proline

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0136741 (3-Hydroxy-L-proline)

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PDB for NP0136741 (3-Hydroxy-L-proline)
HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  O   UNK     0      -1.896   1.799   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.635   0.281   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.818  -0.704   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.189  -0.251   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.229  -1.733   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.768  -1.793   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.300  -0.348   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.091   0.605   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.150   2.144   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    4    9                                                  
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0136741 (3-Hydroxy-L-proline)
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SMILES for NP0136741 (3-Hydroxy-L-proline)
O[C@H]1CCN[C@H]1C(O)=O
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INCHI for NP0136741 (3-Hydroxy-L-proline)
InChI=1S/C5H9NO3/c7-3-1-2-6-4(3)5(8)9/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4+/m0/s1
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View in JSmol
Synonyms
ValueSource
cis-3-Hydroxy-D-prolineChEBI
Procollagen trans-3-hydroxy-L-prolineHMDB
Chemical FormulaC5H9NO3
Average Mass131.1299 Da
Monoisotopic Mass131.05824 Da
IUPAC Name(2R,3S)-3-hydroxypyrrolidine-2-carboxylic acid
Traditional Name3-hydroxy-L-proline
CAS Registry NumberNot Available
SMILES
O[C@H]1CCN[C@H]1C(O)=O
InChI Identifier
InChI=1S/C5H9NO3/c7-3-1-2-6-4(3)5(8)9/h3-4,6-7H,1-2H2,(H,8,9)/t3-,4+/m0/s1
InChI KeyBJBUEDPLEOHJGE-IUYQGCFVSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Brachystegia longifoliaLOTUS 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
    • 

  • Beta-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Pyrrolidine
    • 

  • Amino acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Secondary amine
    • 

  • Secondary aliphatic amine
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic oxide
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Amine
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
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-3.2ALOGPS
logP-3.7ChemAxon
logS0.52ALOGPS
pKa (Strongest Acidic)1.61ChemAxon
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
Polarizability12.27 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002113  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB011875  
KNApSAcK IDNot Available
Chemspider ID9312313  
KEGG Compound IDC04397  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6494  
PubChem Compound11137200  
PDB IDNot Available
ChEBI ID87840  
Good Scents IDNot Available
References
General References
  1. Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP: Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. Elife. 2014 Jun 30;3. doi: 10.7554/eLife.03275. [PubMed:24980702  ]