Structure of PDB 4p9s Chain A Binding Site BS01

Receptor Information

>4p9s Chain A (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 A 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 A79 G80 S81 T82 H84 A85 L88 V212 A241 G242 W244 H263 Y265 G363 I365 F390 Y392 G393 I394 I395
• Binding residue (residue number reindexed from 1): I11 G12 G14 C15 V16 L35 E36 K37 A42 G43 S44 T45 H47 A48 L51 V175 A204 G205 W207 H226 Y228 G326 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)