Structure of PDB 5l46 Chain B Binding Site BS01

Receptor Information

>5l46 Chain B (length=808) Species: 9606 (Homo sapiens)

KDRAETVIIGGGCVGVSLAYHLAKAGMKDVVLLEKSELTAGSTWHAAGLT
TYFHPGINLKKIHYDSIKLYEKLEEETGQVVGFHQPGSIRLATTPVRVDE
FKYQMTRTGWHATEQYLIEPEKIQEMFPLLNMNKVLAGLYNPGDGHIDPY
SLTMALAAGARKCGALLKYPAPVTSLKARSDGTWDVETPQGSMRANRIVN
AAGFWAREVGKMIGLEHPLIPVQHQYVVTSTIPEVKALKRELPVLRDLEG
SYYLRQERDGLLFGPYESQEKMKVQDSWVTNGVPPGFGKELFESDLDRIM
EHIKAAMEMVPVLKKADIINVVNGPITYSPDILPMVGPHQGVRNYWVAIG
FGYGIIHAGGVGKYLSDWILHGEPPFDLIELDPNRYGKWTTTQYTEAKAR
ESYGFNNIVGYPKEERFAGRPTQRVSGLYQRLESKCSMGFHAGWEQPHWF
YKPGQDTQYRPSFRRTNWFEPVGSEYKQVMQRVAVTDLSPFGKFNIKGQD
SIRLLDHLFANVIPKVGFTNISHMLTPKGRVYAELTVSHQSPGEFLLITG
SGSELHDLRWIEEEAVKGGYDVEIKNITDELGVLGVAGPQARKVLQKLTS
EDLSDDVFKFLQTKSLKVSNIPVTAIRISYTGELGWELYHRREDSVALYD
AIMNAGQEEGIDNFGTYAMNALRLEKAFRAWGLEMNCDTNPLEAGLEYFV
KLNKPADFIGKQALKQIKAKGLKRRLVCLTLATDDVDPEGNESIWYNGKV
VGNTTSGSYSYSIQKSLAFAYVPVQLSEVGQQVEVELLGKNYPAVIIQEP
LVLTEPTR

Ligand information

• Ligand ID: FAD
• InChI: InChI=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
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=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 1.5.0: Cc1cc2c(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 1.5.0: Cc1cc2c(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 3.341: Cc1cc2N=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 10.04: O=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
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 5l46 Chain B Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5l46 Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant.
• Resolution: 3.09 Å
• Binding residue (original residue number in PDB): I55 G56 G57 G58 V60 L79 E80 K81 G87 S88 T89 H91 L95 V219 A248 G249 W251 Y272 I372 F397 Y399 G400 I401 I402
• Binding residue (residue number reindexed from 1): I9 G10 G11 G12 V14 L33 E34 K35 G41 S42 T43 H45 L49 V173 A202 G203 W205 Y226 I326 F351 Y353 G354 I355 I356
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): T97 E146 H270 Y299 E580
• Catalytic site (residue number reindexed from 1): T51 E100 H224 Y253 E534
• Enzyme Commision number: 1.5.8.4: dimethylglycine dehydrogenase.

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0047865 dimethylglycine dehydrogenase activity

Biological Process

• GO:0006579 amino-acid betaine catabolic process
• GO:0019695 choline metabolic process
• GO:0042426 choline catabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix

External links

• PDB: RCSB:5l46, PDBe:5l46, PDBj:5l46
• PDBsum: 5l46
• PubMed: 27486859
• UniProt: Q9UI17|M2GD_HUMAN Dimethylglycine dehydrogenase, mitochondrial (Gene Name=DMGDH)