Structure of PDB 1vdc Chain A Binding Site BS01

Receptor Information
>1vdc Chain A (length=322) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LETHNTRLCIVGSGPAAHTAAIYAARAELKPLLFEGWMANDIAPGGQLTT
TTDVENFPGFPEGILGVELTDKFRKQSERFGTTIFTETVTKVDFSSKPFK
LFTDSKAILADAVILAIGAVAKRLSFVGSGEVLGGFWNRGISACAVCDGA
APIFRNKPLAVIGGGDSAMEEANFLTKYGSKVYIIHRRDAFRASKIMQQR
ALSNPKIDVIWNSSVVEAYGDGERDVLGGLKVKNVVTGDVSDLKVSGLFF
AIGHEPATKFLDGGVELDSDGYVVTKPGTTQTSVPGVFAAGDVQDKKYRQ
AITAAGTGCMAALDAEHYLQEI
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 chain1vdc Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1vdc Crystal structure of Arabidopsis thaliana NADPH dependent thioredoxin reductase at 2.5 A resolution.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G12 S13 G14 P15 A16 F34 E35 G36 A36C I37 G41 Q42 L43 V49 N51 T83 V84 I112 G113 C138 G285 D286 R293 Q294 A295 A298
Binding residue
(residue number reindexed from 1)		G12 S13 G14 P15 A16 F34 E35 G36 A39 I42 G46 Q47 L48 V54 N56 T88 V89 I117 G118 C147 G291 D292 R299 Q300 A301 A304
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C135 C138 D139
Catalytic site (residue number reindexed from 1) C144 C147 D148
Enzyme Commision number 1.8.1.9: thioredoxin-disulfide reductase.
Gene Ontology
Molecular Function
GO:0004791 thioredoxin-disulfide reductase (NADPH) activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0019430 removal of superoxide radicals
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1vdc, PDBe:1vdc, PDBj:1vdc
PDBsum1vdc
PubMed9000629
UniProtQ39243|TRXB1_ARATH Thioredoxin reductase 1, mitochondrial (Gene Name=NTR1)

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