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Showing metabocard for Penicillamine (HMDB0014997)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:51 UTC
Update Date2023-02-21 17:18:22 UTC
HMDB IDHMDB0014997
Secondary Accession Numbers
  • HMDB14997
Metabolite Identification
Common NamePenicillamine
DescriptionPenicillamine is only found in individuals that have used or taken this drug. It is the most characteristic degradation product of the penicillin antibiotics. It is used as an antirheumatic and as a chelating agent in Wilson's disease. [PubChem]Penicillamine is a chelating agent recommended for the removal of excess copper in patients with Wilson's disease. From in vitro studies which indicate that one atom of copper combines with two molecules of penicillamine. Penicillamine also reduces excess cystine excretion in cystinuria. This is done, at least in part, by disulfide interchange between penicillamine and cystine, resulting in formation of penicillamine-cysteine disulfide, a substance that is much more soluble than cystine and is excreted readily. Penicillamine interferes with the formation of cross-links between tropocollagen molecules and cleaves them when newly formed. The mechanism of action of penicillamine in rheumatoid arthritis is unknown although it appears to suppress disease activity. Unlike cytotoxic immunosuppressants, penicillamine markedly lowers IgM rheumatoid factor but produces no significant depression in absolute levels of serum immunoglobulins. Also unlike cytotoxic immunosuppressants which act on both, penicillamine in vitro depresses T-cell activity but not B-cell activity.
Structure
Data?1676999902
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0014997 (Penicillamine)

  Mrv0541 04191212152D          

  9  8  0  0  1  0            999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4290    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4290    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  1  5  1  0  0  0  0
  4  2  1  0  0  0  0
  7  2  2  0  0  0  0
  6  3  1  0  0  0  0
  8  3  1  0  0  0  0
  3  9  1  0  0  0  0
M  END
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3D MOL for HMDB0014997 (Penicillamine)

HMDB0253908
     RDKit          3D
L-Penicillamine
 20 19  0  0  0  0  0  0  0  0999 V2000
   -0.8531   -0.7869   -1.2127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7617    0.1225   -0.0206 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3476   -0.6377    1.1750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7590    1.5752   -0.3139 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.6669    0.4361    0.3595 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3195   -0.8078    0.6713 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3698    1.2338   -0.6367 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8941    2.3357   -0.9857 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5453    0.7759   -1.1860 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1504   -1.0803   -1.6007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3965   -1.7473   -0.9795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4605   -0.3329   -2.0449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8564   -0.2869    2.0959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1682   -1.7264    1.0050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4610   -0.5294    1.2054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6932    1.7733    0.7224 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6259    1.0257    1.3079 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6834   -1.2100   -0.2246 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1287   -0.6649    1.3234 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3732    0.5323   -0.6604 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  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
  1 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  6 18  1  0
  6 19  1  0
  9 20  1  0
M  END
Download

3D SDF for HMDB0014997 (Penicillamine)

  Mrv0541 04191212152D          

  9  8  0  0  1  0            999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4290    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4290    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  1  5  1  0  0  0  0
  4  2  1  0  0  0  0
  7  2  2  0  0  0  0
  6  3  1  0  0  0  0
  8  3  1  0  0  0  0
  3  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014997

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)(S)C(N)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO2S/c1-5(2,9)3(6)4(7)8/h3,9H,6H2,1-2H3,(H,7,8)

> <INCHI_KEY>
VVNCNSJFMMFHPL-UHFFFAOYSA-N

> <FORMULA>
C5H11NO2S

> <MOLECULAR_WEIGHT>
149.211

> <EXACT_MASS>
149.051049291

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
14.88364366068771

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-3-methyl-3-sulfanylbutanoic acid

> <ALOGPS_LOGP>
-1.70

> <JCHEM_LOGP>
-2.146518265659755

> <ALOGPS_LOGS>
-1.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.076558230275829

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.555552931139977

> <JCHEM_PKA_STRONGEST_BASIC>
9.093679244005854

> <JCHEM_POLAR_SURFACE_AREA>
63.32

> <JCHEM_REFRACTIVITY>
37.22500000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.65e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(+-)-penicillamine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0014997 (Penicillamine)

HMDB0253908
     RDKit          3D
L-Penicillamine
 20 19  0  0  0  0  0  0  0  0999 V2000
   -0.8531   -0.7869   -1.2127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7617    0.1225   -0.0206 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3476   -0.6377    1.1750 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7590    1.5752   -0.3139 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.6669    0.4361    0.3595 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3195   -0.8078    0.6713 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3698    1.2338   -0.6367 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8941    2.3357   -0.9857 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5453    0.7759   -1.1860 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1504   -1.0803   -1.6007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3965   -1.7473   -0.9795 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4605   -0.3329   -2.0449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8564   -0.2869    2.0959 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1682   -1.7264    1.0050 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4610   -0.5294    1.2054 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6932    1.7733    0.7224 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6259    1.0257    1.3079 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6834   -1.2100   -0.2246 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1287   -0.6649    1.3234 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3732    0.5323   -0.6604 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  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
  1 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  6 18  1  0
  6 19  1  0
  9 20  1  0
M  END
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PDB for HMDB0014997 (Penicillamine)

HEADER    PROTEIN                                 19-APR-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       0.000  -1.540   0.000  0.00  0.00           N+0
HETATM    6  S   UNK     0      -1.334   2.310   0.000  0.00  0.00           S+0
HETATM    7  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    3    5                                                  
CONECT    2    1    4    7                                                  
CONECT    3    1    6    8    9                                             
CONECT    4    2                                                            
CONECT    5    1                                                            
CONECT    6    3                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    3                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0014997 (Penicillamine)

COMPND    HMDB0014997
HETATM    1  C1  UNL     1      -1.898   0.478   0.348  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.540  -0.225   0.311  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.726  -1.535  -0.364  1.00  0.00           C  
HETATM    4  S1  UNL     1      -0.018  -0.426   2.038  1.00  0.00           S  
HETATM    5  C4  UNL     1       0.403   0.712  -0.372  1.00  0.00           C  
HETATM    6  N1  UNL     1       0.438   1.927   0.420  1.00  0.00           N  
HETATM    7  C5  UNL     1       1.743   0.212  -0.594  1.00  0.00           C  
HETATM    8  O1  UNL     1       2.718   0.842  -0.111  1.00  0.00           O  
HETATM    9  O2  UNL     1       2.071  -0.936  -1.314  1.00  0.00           O  
HETATM   10  H1  UNL     1      -2.653  -0.330   0.491  1.00  0.00           H  
HETATM   11  H2  UNL     1      -1.891   1.175   1.214  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.004   0.993  -0.623  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.484  -2.343   0.381  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.800  -1.744  -0.643  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.147  -1.683  -1.273  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.301  -1.797   2.247  1.00  0.00           H  
HETATM   17  H8  UNL     1      -0.008   1.031  -1.376  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.931   1.768   1.316  1.00  0.00           H  
HETATM   19  H10 UNL     1       0.734   2.753  -0.106  1.00  0.00           H  
HETATM   20  H11 UNL     1       2.830  -0.871  -1.988  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    4    5
CONECT    3   13   14   15
CONECT    4   16
CONECT    5    6    7   17
CONECT    6   18   19
CONECT    7    8    8    9
CONECT    9   20
END
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SMILES for HMDB0014997 (Penicillamine)

CC(C)(S)C(N)C(O)=O
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INCHI for HMDB0014997 (Penicillamine)

InChI=1S/C5H11NO2S/c1-5(2,9)3(6)4(7)8/h3,9H,6H2,1-2H3,(H,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC5H11NO2S
Average Molecular Weight149.211
Monoisotopic Molecular Weight149.051049291
IUPAC Name2-amino-3-methyl-3-sulfanylbutanoic acid
Traditional Name(+-)-penicillamine
CAS Registry Number52-67-5
SMILES
CC(C)(S)C(N)C(O)=O
InChI Identifier
InChI=1S/C5H11NO2S/c1-5(2,9)3(6)4(7)8/h3,9H,6H2,1-2H3,(H,7,8)
InChI KeyVVNCNSJFMMFHPL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as valine and derivatives. Valine and derivatives are compounds containing valine or a derivative thereof resulting from reaction of valine 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 ParentValine and derivatives
Alternative Parents
Substituents
  • Valine or derivatives
  • Alpha-amino acid
  • Branched fatty acid
  • Thia fatty acid
  • Methyl-branched fatty acid
  • Fatty acid
  • Fatty acyl
  • Amino acid
  • Alkylthiol
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Primary amine
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Organic oxygen compound
  • Amine
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point198.5 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility4.65 g/LNot Available
LogP-1.9Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00859 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00859 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID4565
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPenicillamine
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID50868
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Munro R, Capell HA: Penicillamine. Br J Rheumatol. 1997 Jan;36(1):104-9. [PubMed:9117147 ]
  2. Suarez-Almazor ME, Spooner C, Belseck E: Penicillamine for rheumatoid arthritis. Cochrane Database Syst Rev. 2000;(2):CD001460. [PubMed:10796440 ]
  3. Walshe JM: The story of penicillamine: a difficult birth. Mov Disord. 2003 Aug;18(8):853-9. [PubMed:12889074 ]
  4. WALSHE JM: Penicillamine, a new oral therapy for Wilson's disease. Am J Med. 1956 Oct;21(4):487-95. [PubMed:13362281 ]
  5. Gong Y, Frederiksen SL, Gluud C: D-penicillamine for primary biliary cirrhosis. Cochrane Database Syst Rev. 2004 Oct 18;(4):CD004789. [PubMed:15495127 ]
  6. Duruelo J, Cuende E, Preciado E, Diaz de Otazu R, Vesga JC: [Microscopic polyangiitis in a patient with systemic sclerosis]. Reumatol Clin. 2005 Oct;1(3):177-9. doi: 10.1016/S1699-258X(05)72739-X. Epub 2008 Dec 20. [PubMed:21794259 ]
  7. Masson MJ, Teranishi M, Shenton JM, Uetrecht JP: Investigation of the involvement of macrophages and T cells in D-penicillamine-induced autoimmunity in the Brown Norway rat. J Immunotoxicol. 2004 Apr;1(2):79-93. doi: 10.1080/15476910490496258. [PubMed:18958641 ]

Transporters

Enzyme Details
1. Solute carrier organic anion transporter family member 1B1
General function:
Involved in transporter activity
Specific function:
Mediates the Na(+)-independent transport of organic anions such as pravastatin, taurocholate, methotrexate, dehydroepiandrosterone sulfate, 17-beta-glucuronosyl estradiol, estrone sulfate, prostaglandin E2, thromboxane B2, leukotriene C3, leukotriene E4, thyroxine and triiodothyronine. May play an important role in the clearance of bile acids and organic anions from the liver
Gene Name:
SLCO1B1
Uniprot ID:
Q9Y6L6
Molecular weight:
76448.0
References
  1. Gui C, Hagenbuch B: Role of transmembrane domain 10 for the function of organic anion transporting polypeptide 1B1. Protein Sci. 2009 Nov;18(11):2298-306. doi: 10.1002/pro.240. [PubMed:19760661 ]