Showing metabocard for D-ornithine (MMDBc0054439)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 23:12:21 UTC
Update Date2024-04-30 20:53:03 UTC
Metabolite IDMMDBc0054439
Metabolite Identification
Common NameD-ornithine
DescriptionD-Ornithine is an amino acid produced in the urea cycle by the splitting off of urea from arginine. Ornithine is one of the products of the action of the enzyme arginase on L-arginine, creating urea. Therefore, ornithine is a central part of the urea cycle, which allows for the disposal of excess nitrogen. D-Ornithine has been identified in the human placenta (PMID: 32033212 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007feca7722400>

      
  Mrv1652311091717012D          

  9  8  0  0  1  0            999 V2000
   25.1625  -14.2627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.4480  -13.0251    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7336  -15.0877    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.8757  -14.2627    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.7336  -14.2627    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   21.5902  -13.8501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0191  -13.8501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.3046  -14.2627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.4480  -13.8501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2  9  2  0  0  0  0
  5  3  1  6  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  9  1  0  0  0  0
  6  8  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007feca7722400>

HMDB0003374
     RDKit          3D
D-Ornithine
 21 20  0  0  0  0  0  0  0  0999 V2000
   -3.1487   -0.2607    0.3447 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8134    0.2789    0.3453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0444   -0.2575   -0.8420 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649    0.2881   -0.8758 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1587   -0.0714    0.3571 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2542   -1.5125    0.4901 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5288    0.4963    0.1594 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5252   -0.2707    0.1321 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7055    1.8621    0.0061 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1144   -1.2428   -0.0015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7596    0.3353   -0.2483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8685    1.3892    0.2634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2913    0.0278    1.2936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5432    0.0988   -1.7659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0086   -1.3578   -0.8123 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8710   -0.2387   -1.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4118    1.3539   -1.1122 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7219    0.3436    1.2692 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8979   -1.9811   -0.3676 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2417   -1.7579    0.6842 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9103    2.4772   -0.1143 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
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  1
  6 19  1  0
  6 20  1  0
  9 21  1  0
M  END
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3D SDF for #<Metabolite:0x00007feca7722400>

      
  Mrv1652311091717012D          

  9  8  0  0  1  0            999 V2000
   25.1625  -14.2627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   24.4480  -13.0251    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7336  -15.0877    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.8757  -14.2627    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.7336  -14.2627    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   21.5902  -13.8501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0191  -13.8501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.3046  -14.2627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.4480  -13.8501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2  9  2  0  0  0  0
  5  3  1  6  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  9  1  0  0  0  0
  6  8  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054439

> <DATABASE_NAME>
MIME

> <SMILES>
NCCC[C@@H](N)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m1/s1

> <INCHI_KEY>
AHLPHDHHMVZTML-SCSAIBSYSA-N

> <FORMULA>
C5H12N2O2

> <MOLECULAR_WEIGHT>
132.161

> <EXACT_MASS>
132.089877638

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
13.736745607390656

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2,5-diaminopentanoic acid

> <ALOGPS_LOGP>
-3.64

> <JCHEM_LOGP>
-3.6582876081320586

> <ALOGPS_LOGS>
0.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.666422703275891

> <JCHEM_PKA_STRONGEST_BASIC>
10.2868213384358

> <JCHEM_POLAR_SURFACE_AREA>
89.33999999999999

> <JCHEM_REFRACTIVITY>
33.2085

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.72e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-(-)-ornithine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007feca7722400>

HMDB0003374
     RDKit          3D
D-Ornithine
 21 20  0  0  0  0  0  0  0  0999 V2000
   -3.1487   -0.2607    0.3447 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8134    0.2789    0.3453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0444   -0.2575   -0.8420 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649    0.2881   -0.8758 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1587   -0.0714    0.3571 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2542   -1.5125    0.4901 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5288    0.4963    0.1594 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5252   -0.2707    0.1321 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7055    1.8621    0.0061 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1144   -1.2428   -0.0015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7596    0.3353   -0.2483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8685    1.3892    0.2634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2913    0.0278    1.2936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5432    0.0988   -1.7659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0086   -1.3578   -0.8123 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8710   -0.2387   -1.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4118    1.3539   -1.1122 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7219    0.3436    1.2692 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8979   -1.9811   -0.3676 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2417   -1.7579    0.6842 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9103    2.4772   -0.1143 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
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  1
  6 19  1  0
  6 20  1  0
  9 21  1  0
M  END
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PDB for #<Metabolite:0x00007feca7722400>

HEADER    PROTEIN                                 09-NOV-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-NOV-17         0                                  
HETATM    1  O   UNK     0      46.970 -26.624   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      45.636 -24.314   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      44.303 -28.164   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0      38.968 -26.624   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      44.303 -26.624   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      40.302 -25.854   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      42.969 -25.854   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      41.635 -26.624   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      45.636 -25.854   0.000  0.00  0.00           C+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3    5                                                            
CONECT    4    6                                                            
CONECT    5    3    7    9                                                  
CONECT    6    4    8                                                       
CONECT    7    5    8                                                       
CONECT    8    6    7                                                       
CONECT    9    1    2    5                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for #<Metabolite:0x00007feca7722400>

COMPND    HMDB0003374
HETATM    1  N1  UNL     1      -3.149  -0.261   0.345  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.813   0.279   0.345  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.044  -0.258  -0.842  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.365   0.288  -0.876  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.159  -0.071   0.357  1.00  0.00           C  
HETATM    6  N2  UNL     1       1.254  -1.513   0.490  1.00  0.00           N  
HETATM    7  C5  UNL     1       2.529   0.496   0.159  1.00  0.00           C  
HETATM    8  O1  UNL     1       3.525  -0.271   0.132  1.00  0.00           O  
HETATM    9  O2  UNL     1       2.705   1.862   0.006  1.00  0.00           O  
HETATM   10  H1  UNL     1      -3.114  -1.243  -0.001  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.760   0.335  -0.248  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.868   1.389   0.263  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.291   0.028   1.294  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.543   0.099  -1.766  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.009  -1.358  -0.812  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.871  -0.239  -1.737  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.412   1.354  -1.112  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.722   0.344   1.269  1.00  0.00           H  
HETATM   19  H10 UNL     1       0.898  -1.981  -0.368  1.00  0.00           H  
HETATM   20  H11 UNL     1       2.242  -1.758   0.684  1.00  0.00           H  
HETATM   21  H12 UNL     1       1.910   2.477  -0.114  1.00  0.00           H  
CONECT    1    2   10   11
CONECT    2    3   12   13
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6    7   18
CONECT    6   19   20
CONECT    7    8    8    9
CONECT    9   21
END
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SMILES for #<Metabolite:0x00007feca7722400>

NCCC[C@@H](N)C(O)=O
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INCHI for #<Metabolite:0x00007feca7722400>

InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m1/s1
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Synonyms
ValueSource
(R)-OrnithineChEBI
(2R)-2,5-DiaminopentanoateHMDB
(2R)-2,5-Diaminopentanoic acidHMDB
OrnithineHMDB
Molecular FormulaC5H12N2O2
Average Mass132.161
Monoisotopic Mass132.089877638
IUPAC Name(2R)-2,5-diaminopentanoic acid
Traditional NameL-(-)-ornithine
CAS Registry NumberNot Available
SMILES
NCCC[C@@H](N)C(O)=O
InChI Identifier
InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m1/s1
InChI KeyAHLPHDHHMVZTML-SCSAIBSYSA-N