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Showing NP-Card for 4-Hydroxyproline (NP0001257)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:39:52 UTC
NP-MRD IDNP0001257
Secondary Accession NumbersNone
Natural Product Identification
Common Name4-Hydroxyproline
Description4-Hydroxyproline (hydroxyproline or Hyp) is a major component of the protein collagen. Hydroxyproline is produced by hydroxylation of the amino acid proline and is, therefore, a post-translationally modified amino acid. Hydroxyproline and proline play key roles for collagen stability. In particular, they permit the sharp twisting of the collagen helix. Hydroxyproline is found in few proteins other than collagen. The only other mammalian protein which includes hydroxyproline is elastin. For this reason, hydroxyproline content has been used as an indicator to determine collagen and/or gelatin amount in tissue or biological samples. Increased serum and urine levels of hydroxyproline have been found in Paget's disease (PMID: 436278 ). Hydroxyproline (Hyp) content in biological fluids is used as a parameter of collagen catabolism, especially bone resorption or tissue degradation. Bedridden and elderly individuals show significantly elevated serum levels of hydroxyproline in comparison to normal, active individuals (PMID: 10706420 ). Elevated levels of urinary hydroxyproline are also indicative of muscle damage (PMID: 21988268 ). Increased reactive oxygen species (ROS) are also known to accelerate collagen degradation. Hydroxyproline levels increase in cases of depression and stress (PMID: 21483218 ). 4-Hydroxyproline is found to be associated with Alzheimer's disease, and also hydroxyprolinemia and iminoglycinuria which are both inborn errors of metabolism. 4-Hydroxyproline is also involved in metabolic disorders such as hyperprolinemia type I, hyperornithinemia with gyrate atrophy (HOGA), L-arginine:Glycine amidinotransferase deficiency, creatine deficiency, and guanidinoacetate methyltransferase deficiency. A deficiency in ascorbic acid can result in impaired hydroxyproline formation (PubChem). Trans-4-Hydroxy-L-proline is a biomarker for the consumption of processed meat.
Structure
Data?1628564084
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0001257 (4-Hydroxyproline)


  Mrv1652310282120122D          

  9  9  0  0  1  0            999 V2000
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  1  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
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1501   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  5  7  1  6  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
Download

3D MOL for NP0001257 (4-Hydroxyproline)

     RDKit          3D

 18 18  0  0  0  0  0  0  0  0999 V2000
    2.2968   -0.0173   -1.4898 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0914   -0.1509   -0.2484 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1078   -0.6721    0.5697 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8125    0.2342    0.3325 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1862   -0.9114    0.3056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4955   -0.2950   -0.1890 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6002   -0.6874    0.5048 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1960    1.1984    0.0382 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1561    1.2312   -0.5429 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7648    0.0531    0.8946 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8649    0.6985    1.3381 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1596   -1.7216   -0.3771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2924   -1.2969    1.3349 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5198   -0.4711   -1.2604 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1264   -1.3686    0.0454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1187    1.3645    1.1316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8680    1.8452   -0.4964 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1493    0.9672   -1.5313 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 NP0001257 (4-Hydroxyproline)


  Mrv1652310282120122D          

  9  9  0  0  1  0            999 V2000
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  1  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
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1501   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  5  7  1  6  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0001257

> <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-DMTCNVIQSA-N

> <FORMULA>
C5H9NO3

> <MOLECULAR_WEIGHT>
131.1299

> <EXACT_MASS>
131.058243159

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.291927113198778

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,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>
1.6413819507648508

> <JCHEM_PKA_STRONGEST_BASIC>
10.617096890348789

> <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>
hypro

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0001257 (4-Hydroxyproline)

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PDB for NP0001257 (4-Hydroxyproline)
HEADER    PROTEIN                                 28-OCT-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-OCT-21         0                                  
HETATM    1  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.830  -0.290   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.011  -2.943   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -2.147  -1.375   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    2                                                       
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0001257 (4-Hydroxyproline)
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SMILES for NP0001257 (4-Hydroxyproline)
O[C@H]1CN[C@@H](C1)C(O)=O
Download
INCHI for NP0001257 (4-Hydroxyproline)
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
Download
View in JSmol
Synonyms
ValueSource
(2S,4R)-4-Hydroxy-2-pyrrolidinecarboxylic acidChEBI
(2S,4R)-trans-4-HydroxyprolineChEBI
delta-HydroxyprolineChEBI
Hydroxy-L-prolineChEBI
HydroxyprolineChEBI
HypChEBI
HyproChEBI
L-4-HydroxyprolineChEBI
L-Threo-4-hydroxyprolineChEBI
trans-HydroxyprolineChEBI
trans-L-HydroxyprolineChEBI
L-HydroxyprolineKegg
trans-4-Hydroxy-L-prolineKegg
(2S,4R)-4-Hydroxy-2-pyrrolidinecarboxylateGenerator
Δ-hydroxyprolineGenerator
(2S,4R)-4-Hydroxypyrrolidine-2-carboxylic acidHMDB
(4R)-4-Hydroxy-L-prolineHMDB
4-Hydroxy-2-pyrrolidinecarboxylic acidHMDB
4-Hydroxy-L-prolineHMDB
4-L-HydroxyprolineHMDB
HydroxiprolineHMDB
Hydroxy-prolineHMDB
LS-HydroxyprolineHMDB
OxaceprolHMDB
trans-4-HydroxyprolineHMDB
4 HydroxyprolineHMDB
OxyprolineHMDB
(-)-4-Hydroxy-2-pyrrolidinecarboxylic acidHMDB
(2S,4R)-(-)-4-HydroxyprolineHMDB
(2S,4R)-4-HydroxyprolineHMDB
(R)-4-Hydroxy-(S)-prolineHMDB
(R)-4-Hydroxy-L-prolineHMDB
(S)-HydroxyprolineHMDB
4(R)-Hydroxy-2(S)-pyrrolidinecarboxylic acidHMDB
4(R)-HydroxyprolineHMDB
4-Hydroxy-(S)-prolineHMDB
4-trans-Hydroxy-L-prolineHMDB
L-HyproHMDB
L-trans-4-HydroxyprolineHMDB
NSC 46704HMDB
trans-L-4-HydroxyprolineHMDB
4-HydroxyprolineHMDB
Chemical FormulaC5H9NO3
Average Mass131.1299 Da
Monoisotopic Mass131.05824 Da
IUPAC Name(2S,4R)-4-hydroxypyrrolidine-2-carboxylic acid
Traditional Namehypro
CAS Registry Number51-35-4
SMILES
[H]OC(=O)[C@@]1([H])N([H])C([H])([H])[C@]([H])(O[H])C1([H])[H]
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-DMTCNVIQSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)Varshavi.d262021-10-26View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Varshavi.d262021-10-26View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)Varshavi.d262021-10-26View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Varshavi.d262021-10-26View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)Varshavi.d262021-08-09View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)Varshavi.d262021-08-07View Spectrum
Species
Species of Origin
Species NameSourceReference
Afzelia bellaKNApSAcK Database
Allium ampeloprasumFooDB
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Antirrhinum majusLOTUS Database
Arabidopsis thalianaKNApSAcK Database
Arachis hypogaeaFooDB
Bison bisonFooDB
Borago officinalisFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Brassica oleracea var. italicaPlant
Bubalus bubalisFooDB
Cannabis sativaCannabisDB
      Not Available
Capra aegagrus hircusFooDB
Castanea sativaKNApSAcK Database
Ceratonia siliquaFooDB
CervidaeFooDB
Cervus canadensisFooDB
Chlamydomonas reinhardtiiLOTUS Database
CinnamomumFooDB
Citrullus lanatusFooDB
Citrus X sinensis (L.) Osbeck (pro. sp.)FooDB
Cocos nuciferaFooDB
ColumbaFooDB
ColumbidaeFooDB
Curcuma longaFooDB
Daphnia pulexLOTUS Database
Daucus carotaFooDB
Daucus carota ssp. sativusFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Glycine maxFooDB
HippoglossusFooDB
Hippoglossus hippoglossusFooDB
Homo sapiensLOTUS Database
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Linum usitatissimumFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Mus musculusLOTUS Database
Numida meleagrisFooDB
OdocoileusFooDB
Origanum vulgareFooDB
Origanum X majoricumFooDB
OryctolagusFooDB
Ovis ariesFooDB
Phaseolus vulgarisFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Piper nigrum L.FooDB
Prunus domesticaLOTUS Database
Salmo salarFooDB
Santalum albumKNApSAcK Database
Solanum tuberosumFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Syzygium aromaticumFooDB
Vicia fabaKNApSAcK Database
Zea mays L.FooDB
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
    • 

  • L-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
StateSolid
Experimental Properties
PropertyValueReference
Melting Point274 - 275 °CNot Available
Boiling Point186.13 °C. @  760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility361 mg/mL at 25 °CNot Available
LogP-3.17Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility492 g/LALOGPS
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
Polarizability12.29 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000725  
DrugBank IDDB08847  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB013511  
KNApSAcK IDC00001370  
Chemspider ID5605  
KEGG Compound IDC01157  
BioCyc ID4-HYDROXY-L-PROLINE  
BiGG ID36935  
Wikipedia LinkHydroxyproline  
METLIN ID257  
PubChem Compound5810  
PDB IDNot Available
ChEBI ID18095  
Good Scents IDrw1510101  
References
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411  ] 
  2. Cynober LA: Plasma amino acid levels with a note on membrane transport: characteristics, regulation, and metabolic significance. Nutrition. 2002 Sep;18(9):761-6. [PubMed:12297216  ] 
  3. Kelleher PC: Urinary excretion of hydroxyproline, hydroxylysine and hydroxylysine glycosides by patients with Paget's disease of bone and carcinoma with metastases in bone. Clin Chim Acta. 1979 Mar 15;92(3):373-9. [PubMed:436278  ] 
  4. Matsuda Y, Matsumoto K, Yamada A, Ichida T, Asakura H, Komoriya Y, Nishiyama E, Nakamura T: Preventive and therapeutic effects in rats of hepatocyte growth factor infusion on liver fibrosis/cirrhosis. Hepatology. 1997 Jul;26(1):81-9. [PubMed:9214455  ] 
  5. Seibel MJ, Woitge HW: Basic principles and clinical applications of biochemical markers of bone metabolism: biochemical and technical aspects. J Clin Densitom. 1999 Fall;2(3):299-321. [PubMed:10548826  ] 
  6. Akalin FA, Sengun D, Eratalay K, Renda N, Caglayan G: Hydroxyproline and total protein levels in gingiva and gingival crevicular fluid in patients with juvenile, rapidly progressive, and adult periodontitis. J Periodontol. 1993 May;64(5):323-9. [PubMed:8515361  ] 
  7. Akalin FA, Sengun D, Renda N, Eratalay K, Caglayan G: Hydroxyproline and total protein levels in gingiva and gingival crevicular fluid in periodontally healthy human subjects. J Nihon Univ Sch Dent. 1992 Sep;34(3):172-7. [PubMed:1287145  ] 
  8. Lee HS, Shun CT, Chiou LL, Chen CH, Huang GT, Sheu JC: Hydroxyproline content of needle biopsies as an objective measure of liver fibrosis: Emphasis on sampling variability. J Gastroenterol Hepatol. 2005 Jul;20(7):1109-14. [PubMed:15955222  ] 
  9. Akalin FA, Bozkurt FY, Sengun D, Renda N, Kalfa Z, Eratalay K, Velidedeoglu E: Hydroxyproline and total protein levels in gingiva from patients treated with phenytoin and cyclosporine-A. J Nihon Univ Sch Dent. 1996 Mar;38(1):21-30. [PubMed:8648408  ] 
  10. Diaz S, Reyes MV, Zepeda A, Gonzalez GB, Lopez JM, Campino C, Croxatto HB: Norplant((R)) implants and progesterone vaginal rings do not affect maternal bone turnover and density during lactation and after weaning. Hum Reprod. 1999 Oct;14(10):2499-505. [PubMed:10527977  ] 
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