Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T77009 | Target Info | |||
| Target Name | Thioredoxin reductase (PRDX5) | ||||
| Synonyms | Thioredoxin peroxidase PMP20; TPx type VI; SBBI10; PrxV; Prx-V; Peroxisomal antioxidant enzyme; Peroxiredoxin5, mitochondrial; Peroxiredoxin-5, mitochondrial; Peroxiredoxin V; PLP; Liver tissue 2Dpage spot 71B; Liver tissue 2D-page spot 71B; Antioxidant enzyme B166; Alu corepressor 1; AOEB166; ACR1 | ||||
| Target Type | Successful Target | ||||
| Gene Name | PRDX5 | ||||
| Biochemical Class | Peroxide acceptor oxidoreductase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Catechol | Ligand Info | |||||
| Structure Description | HUMAN PEROXIREDOXIN 5 with a fragment | PDB:4K7I | ||||
| Method | X-ray diffraction | Resolution | 2.25 Å | Mutation | No | [1] |
| PDB Sequence |
SAPIKVGDAI
9 PAVEVFEGEP19 GNKVNLAELF29 KGKKGVLFGV39 PGAFTPGCSK49 THLPGFVEQA 59 EALKAKGVQV69 VACLSVNDAF79 VTGEWGRAHK89 AEGKVRLLAD99 PTGAFGKETD 109 LLLDDSLVSI119 FGNRRLKRFS129 MVVQDGIVKA139 LNVEPDGTGL149 TCSLAPNIIS 159 QL
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| Ligand Name: (4S,5S)-1,2-Dithiane-4,5-diol | Ligand Info | |||||
| Structure Description | wild type human PrxV with DTT bound as a competitive inhibitor | PDB:3MNG | ||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [2] |
| PDB Sequence |
APIKVGDAIP
10 AVEVFEGEPG20 NKVNLAELFK30 GKKGVLFGVP40 GAFTPGCSKT50 HLPGFVEQAE 60 ALKAKGVQVV70 ACLSVNDAFV80 TGEWGRAHKA90 EGKVRLLADP100 TGAFGKETDL 110 LLDDSLVSIF120 GNRRLKRFSM130 VVQDGIVKAL140 NVEPDGTGLT150 CSLAPNIISQ 160 L
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| Ligand Name: [1,1'-Biphenyl]-3,4-diol | Ligand Info | |||||
| Structure Description | Human Pdrx5 complex with a ligand BP7 | PDB:4MMM | ||||
| Method | X-ray diffraction | Resolution | 1.47 Å | Mutation | No | [1] |
| PDB Sequence |
SAPIKVGDAI
9 PAVEVFEGEP19 GNKVNLAELF29 KGKKGVLFGV39 PGAFTPGCSK49 THLPGFVEQA 59 EALKAKGVQV69 VACLSVNDAF79 VTGEWGRAHK89 AEGKVRLLAD99 PTGAFGKETD 109 LLLDDSLVSI119 FGNRRLKRFS129 MVVQDGIVKA139 LNVEPDGTGL149 TCSLAPNIIS 159 QL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BP7 or .BP72 or .BP73 or :3BP7;style chemicals stick;color identity;select .A:40 or .A:44 or .A:45 or .A:46 or .A:47 or .A:116 or .A:119 or .A:120 or .A:127 or .A:147; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-tert-Butylcatechol | Ligand Info | |||||
| Structure Description | HUMAN PEROXIREDOXIN 5 with a fragment | PDB:4K7O | ||||
| Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [1] |
| PDB Sequence |
SAPIKVGDAI
9 PAVEVFEGEP19 GNKVNLAELF29 KGKKGVLFGV39 PGAFTPGCSK49 THLPGFVEQA 59 EALKAKGVQV69 VACLSVNDAF79 VTGEWGRAHK89 AEGKVRLLAD99 PTGAFGKETD 109 LLLDDSLVSI119 FGNRRLKRFS129 MVVQDGIVKA139 LNVEPDGTGL149 TCSLAPNIIS 159 QL
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EKZ or .EKZ2 or .EKZ3 or :3EKZ;style chemicals stick;color identity;select .A:40 or .A:41 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:116 or .A:119 or .A:120 or .A:127 or .A:147; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-Methylcatechol | Ligand Info | |||||
| Structure Description | HUMAN PEROXIREDOXIN 5 with a fragment | PDB:4K7N | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [1] |
| PDB Sequence |
APIKVGDAIP
10 AVEVFEGEPG20 NKVNLAELFK30 GKKGVLFGVP40 GAFTPGCSKT50 HLPGFVEQAE 60 ALKAKGVQVV70 ACLSVNDAFV80 TGEWGRAHKA90 EGKVRLLADP100 TGAFGKETDL 110 LLDDSLVSIF120 GNRRLKRFSM130 VVQDGIVKAL140 NVEPDGTGLT150 CSLAPNIISQ 160 L
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MCT or .MCT2 or .MCT3 or :3MCT;style chemicals stick;color identity;select .A:40 or .A:44 or .A:45 or .A:46 or .A:47 or .A:116 or .A:119 or .A:120 or .A:127 or .A:147; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Comparing binding modes of analogous fragments using NMR in fragment-based drug design: application to PRDX5. PLoS One. 2014 Jul 15;9(7):e102300. | ||||
| REF 2 | Structural evidence that peroxiredoxin catalytic power is based on transition-state stabilization. J Mol Biol. 2010 Sep 10;402(1):194-209. | ||||
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