Structure of PDB 4kto Chain D Binding Site BS02

Receptor Information
>4kto Chain D (length=374) Species: 266834 (Sinorhizobium meliloti 1021) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MFEAGLNFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREM
GELGLLGITADEAHGGAGLGYLAHCVAMEEISRASASVGLSYGAHSNLCV
NQINRNGKPAQKSRYLPKLISGEHVGALAMSEPGVSMKLKADKRGDRYVL
NGSKMWITNGPDADVLVVYAKTDPGITAFLVEKAFPGFSAGQKLDKLGMR
GSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLDYERVVLSAGPLGIMA
ACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVYAVAAA
CDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRD
AKLYEIGAGTSEIRRMLIGRELFA
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 chain4kto Chain D Residue 401 [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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PDB4kto Crystal structure of a Putative Isovaleryl-CoA dehydrogenase from Sinorhizobium meliloti 1021
Resolution2.137 Å
Binding residue
(original residue number in PDB)		L128 M130 S131 W161 T163 L363 I366 A368 G369 E372
Binding residue
(residue number reindexed from 1)		L128 M130 S131 W156 T158 L353 I356 A358 G359 E362
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) M130 S131 E247 A368 R380
Catalytic site (residue number reindexed from 1) M130 S131 E237 A358 R370
Enzyme Commision number 1.3.8.4: isovaleryl-CoA dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003995 acyl-CoA dehydrogenase activity
GO:0008470 3-methylbutanoyl-CoA dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0016937 short-chain fatty acyl-CoA dehydrogenase activity
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0006552 L-leucine catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4kto, PDBe:4kto, PDBj:4kto
PDBsum4kto
PubMed
UniProtQ92VK1

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