Structure of PDB 4p9s Chain B Binding Site BS01

Receptor Information

>4p9s Chain B (length=816) Species: 10116 (Rattus norvegicus)

EWKDRAETVIIGGGCVGVSLAYHLAKAGMRDVVLLEKSELTAGSTWHAAG
LTTYFHPGINLKKIHYDSIKLYERLEEETGQVVGFHQPGSIRLATTPERV
DEFKYQMTRTNWHATEQYIIEPEKIHELFPLLNMDKILAGLYNPGDGHID
PYSLTMALATGARKYGALLKYPAPVTSLKPRPDGTWDVETPQGSVRANRI
VNAAGFWAREVGKMIGLDHPLIPVQHQYVITSTIPEVKALKRELPVLRDL
EGSYYLRQERDGLLFGPYESQEKMKLQASWVAHGVPPGFGKELFESDLDR
ITEHVEAAMEMVPVLKKADIINIVNGPITYSPDILPMVGPHQGVRNYWVA
IGFGYGIIHAGGVGTYLSDWILHGEPPFDLIELDPNRYGKWTTTQYTEAK
ARESYGFNNIVGYPKEERFAGRPTQRVSGLYKILESKCSMGFHAGWEQPH
WFYKPGQDTQYRPSFRRTNWFEPVGSEYKQVMQRVGVIDLSPFGKFNIKG
QDSTQLLDHLCANVIPKVGFTNISHMLTPRGRVYAELTVSHQSPGEFLLI
TGSGSELHDLRWIEEAAVRGGYDVEIRNITDELGVLGVAGPYARRVLQKL
TSEDLSDDVFKFLQTKSLKISDIPVTAIRISYTGELGWELYHRREDSAAL
YERIMNAGQEEGIDNFGTYALNALRLEKAFRAWGSEMNCDTNPLEAGLDY
FIKLNKPANFTGKQALKQIKAKGLKRRLVCLTLATDNVDPEGNESVWYKG
KVIGNTTSGSYSYSIQKSLAFAYVPVELSEVGQQVEVELLGKNYPATIIQ
EPLVLTEPTRTRLQKD

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: 4p9s Chain B Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4p9s Folate in demethylation: The crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate.
• Resolution: 2.32 Å
• Binding residue (original residue number in PDB): I48 G49 G51 C52 V53 L72 E73 K74 G80 S81 T82 H84 A85 A86 G87 L88 P211 V212 A241 G242 W244 H263 Y265 G363 P364 I365 F390 Y392 G393 I394 I395
• Binding residue (residue number reindexed from 1): I11 G12 G14 C15 V16 L35 E36 K37 G43 S44 T45 H47 A48 A49 G50 L51 P174 V175 A204 G205 W207 H226 Y228 G326 P327 I328 F353 Y355 G356 I357 I358
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): W83 A86 G87 T90 E139 H263 Y292 E573
• Catalytic site (residue number reindexed from 1): W46 A49 G50 T53 E102 H226 Y255 E536
• Enzyme Commision number: 1.5.8.4: dimethylglycine dehydrogenase.

Gene Ontology

Molecular Function

• GO:0005542 folic acid binding
• GO:0016491 oxidoreductase activity
• GO:0047865 dimethylglycine dehydrogenase activity
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0006579 amino-acid betaine catabolic process
• GO:0019695 choline metabolic process
• GO:0035999 tetrahydrofolate interconversion
• GO:0042426 choline catabolic process

Cellular Component

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

External links

• PDB: RCSB:4p9s, PDBe:4p9s, PDBj:4p9s
• PDBsum: 4p9s
• PubMed: 24858690
• UniProt: Q63342|M2GD_RAT Dimethylglycine dehydrogenase, mitochondrial (Gene Name=Dmgdh)