Structure of PDB 2yqu Chain B Binding Site BS03

Receptor Information
>2yqu Chain B (length=455) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MYDLLVIGAGPGGYVAAIRAAQLGMKVGVVEKEKALGGTCLRVGCIPSKA
LLETTERIYEAKKGLLGAKVKGVELDLPALMAHKDKVVQANTQGVEFLFK
KNGIARHQGTARFLSERKVLVEETGEELEARYILIATGSAPLIPPWAQVD
YERVVTSTEALSFPEVPKRLIVVGGGVIGLELGVVWHRLGAEVIVLEYMD
RILPTMDLEVSRAAERVFKKQGLTIRTGVRVTAVVPEAKGARVELEGGEV
LEADRVLVAVGRRPYTEGLSLENAGLSTDERGRIPVDEHLRTRVPHIYAI
GDVVRGPMLAHKASEEGIAAVEHMVRGFGHVDYQAIPSVVYTHPEIAAVG
YTEEELKAQGIPYKVGKFPYSASGRARAMGETEGFIKVLAHAKTDRILGV
HGIGARVGDVLAEAALALFFKASAEDLGRAPHAHPSLSEILKEAALAAWE
RPIHL
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 chain2yqu Chain B Residue 1602 [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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PDB2yqu Crystal structures and evolutionary relationship of two different lipoamide dehydrogenase(E3s) from Thermus thermophilus
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G8 G10 P11 G12 E31 K32 G38 T39 C40 R42 G44 C45 K49 T110 A111 T137 G138 I178 Y265 G301 D302 M308 L309 A310 H311
Binding residue
(residue number reindexed from 1)		G8 G10 P11 G12 E31 K32 G38 T39 C40 R42 G44 C45 K49 T110 A111 T137 G138 I178 Y265 G301 D302 M308 L309 A310 H311
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) P11 L36 C40 C45 S48 G72 V73 V177 E181 S314 H432 H434 E439
Catalytic site (residue number reindexed from 1) P11 L36 C40 C45 S48 G72 V73 V177 E181 S314 H432 H434 E439
Enzyme Commision number 1.8.1.4: dihydrolipoyl dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004148 dihydrolipoyl dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0050660 flavin adenine dinucleotide binding

View graph for
Molecular Function
External links
PDB RCSB:2yqu, PDBe:2yqu, PDBj:2yqu
PDBsum2yqu
PubMed
UniProtQ5SLK6

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