Structure of PDB 4kpr Chain F Binding Site BS01

Receptor Information
>4kpr Chain F (length=485) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SYDFDLIIIGGGSGGLAAAKEAAKFDKKVMVLDFVTPTPLGTRWGLGGTC
VNVGCIPKKLMHQAALLGQALKDSRNYGWKLEDTVKHDWEKMTESVQNHI
GSLNWGYRVALREKKVVYENAYGKFIGPHKIMATNNKGKEKVYSAERFLI
ATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFL
AGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPTKIEQI
EAGTPGRLKVTAKSTNSEETIEDEFNTVLLAVGRDSCTRTIGLETVGVKI
NEKTGKIPVTDEEQTNVPYIYAIGDILEGKLELTPVAIQAGRLLAQRLYG
GSTVKCDYDNVPTTVFTPLEYGCCGLSEEKAVEKFGEENIEVYHSFFWPL
EWTVPSRDNNKCYAKVICNLKDNERVVGFHVLGPNAGEVTQGFAAALKCG
LTKQQLDSTIGIHPVCAEIFTTLSVTKRSGGDILQ
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 chain4kpr Chain F Residue 505 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4kpr The Trp114 residue of thioredoxin reductase 1 is an electron relay sensor for oxidative stress
Resolution2.4 Å
Binding residue
(original residue number in PDB)		I18 G21 S22 G23 D42 F43 T58 C59 G63 C64 K67 Y131 G132 T161 G162 Y200 V201 R293 G333 D334 E341 L342 T343
Binding residue
(residue number reindexed from 1)		I9 G12 S13 G14 D33 F34 T49 C50 G54 C55 K58 Y122 G123 T152 G153 Y191 V192 R284 G324 D325 E332 L333 T334
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C59 C64 G470
Catalytic site (residue number reindexed from 1) C50 C55 G461
Enzyme Commision number 1.11.1.2: NADPH peroxidase.
1.8.1.9: thioredoxin-disulfide reductase.
Gene Ontology
Molecular Function
GO:0004791 thioredoxin-disulfide reductase (NADPH) activity
GO:0016174 NAD(P)H oxidase H2O2-forming activity
GO:0016491 oxidoreductase activity
GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0033797 selenate reductase activity
GO:0042802 identical protein binding
GO:0045340 mercury ion binding
GO:0050137 NADPH peroxidase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0071949 FAD binding
Biological Process
GO:0001707 mesoderm formation
GO:0006979 response to oxidative stress
GO:0007369 gastrulation
GO:0008283 cell population proliferation
GO:0009410 response to xenobiotic stimulus
GO:0010269 response to selenium ion
GO:0016259 selenocysteine metabolic process
GO:0042537 benzene-containing compound metabolic process
GO:0042744 hydrogen peroxide catabolic process
GO:0043065 positive regulation of apoptotic process
GO:0045454 cell redox homeostasis
GO:0048678 response to axon injury
GO:0055093 response to hyperoxia
GO:0070276 halogen metabolic process
GO:0070995 NADPH oxidation
GO:0071280 cellular response to copper ion
GO:0071455 cellular response to hyperoxia
GO:0098869 cellular oxidant detoxification
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0043025 neuronal cell body

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4kpr, PDBe:4kpr, PDBj:4kpr
PDBsum4kpr
PubMed
UniProtO89049|TRXR1_RAT Thioredoxin reductase 1, cytoplasmic (Gene Name=Txnrd1)

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