Structure of PDB 3d8x Chain B Binding Site BS01

Receptor Information
>3d8x Chain B (length=318) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VHNKVTIIGSGPAAHTAAIYLARAEIKPILYEGMMANGIAAGGQLTTTTE
IENFPGFPDGLTGSELMDRMREQSTKFGTEIITETVSKVDLSSKPFKLWT
EFNEDAEPVTTDAIILATGASAKRMHLPGEETYWQKGISACAVCDGAVPI
FRNKPLAVIGGGDSACEEAQFLTKYGSKVFMLVRKDHLRASTIMQKRAEK
NEKIEILYNTVALEAKGDGKLLNALRIKNTKKNEETDLPVSGLFYAIGHT
PATKIVAGQVDTDEAGYIKTVPGSSLTSVPGFFAAGDVQDSKYRQAITSA
GSGCMAALDAEKYLTSLE
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain3d8x Chain B Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3d8x Crystal structure of Saccharomyces cerevisiae cytoplasmic thioredoxin reductase Trr1 reveals the structural basis for species-specific recognition of thioredoxin
Resolution2.8 Å
Binding residue
(original residue number in PDB)		I9 G10 S11 G12 P13 A14 Y32 G34 A37 I40 G44 Q45 L46 T49 I52 N54 T86 V87 T119 W135 C145 G287 D288 R295 Q296 A297 S300
Binding residue
(residue number reindexed from 1)		I8 G9 S10 G11 P12 A13 Y31 G33 A36 I39 G43 Q44 L45 T48 I51 N53 T85 V86 T118 W134 C144 G286 D287 R294 Q295 A296 S299
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C142 C145 D146
Catalytic site (residue number reindexed from 1) C141 C144 D145
Enzyme Commision number 1.8.1.9: thioredoxin-disulfide reductase.
Gene Ontology
Molecular Function
GO:0004791 thioredoxin-disulfide reductase (NADPH) activity
GO:0005515 protein binding
GO:0008198 ferrous iron binding
GO:0016491 oxidoreductase activity
Biological Process
GO:0019430 removal of superoxide radicals
GO:0034599 cellular response to oxidative stress
GO:0045454 cell redox homeostasis
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005758 mitochondrial intermembrane space
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3d8x, PDBe:3d8x, PDBj:3d8x
PDBsum3d8x
PubMed18930846
UniProtP29509|TRXB1_YEAST Thioredoxin reductase 1 (Gene Name=TRR1)

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