Structure of PDB 6myu Chain A Binding Site BS01

Receptor Information

>6myu Chain A (length=611) Species: 9031 (Gallus gallus)

QYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAA
QGGINAALGNMEDDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPAAVIEL
ENYGMPFSRTEEGKIYQRAFGGQSLQFGKGGQAHRCCCVADRTGHSLLHT
LYGRSLRYDTSYFVEYFALDLLMENGECRGVIALCIEDGTIHRFRAKNTV
IATGGYGRTYFSCTSAHTSTGDGTAMVTRAGLPCQDLEFVQFHPTGIYGA
GCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTIEIRE
GRGCGPEKDHVYLQLHHLPPQQLATRLPGISETAMIFAGVDVTKEPIPVL
PTVHYNMGGIPTNYKGQVITHVNGEDKVVPGLYACGEAASASVHGANRLG
ANSLLDLVVFGRACALTIAETCKPGEPVPSIKPNAGEESVANLDKLRFAD
GTIRTSEARLNMQKTMQSHAAVFRTGSILQEGCEKLSQIYRDLAHLKTFD
RGIVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDYKLRIDE
FDYSKPLQGQQKRPFEEHWRKHTLSYVDVKSGKVTLKYRPVIDRTLNEED
CSSVPPAIRSY

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: 6myu Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6myu Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors.
• Resolution: 1.97 Å
• Binding residue (original residue number in PDB): G25 A26 G27 A29 V47 T48 K49 L50 S55 H56 T57 A59 A60 Q61 G62 G63 Y176 F177 A178 A212 T213 G214 D232 L263 H364 Y365 G396 E397 A411 S413 L414 L417
• Binding residue (residue number reindexed from 1): G15 A16 G17 A19 V37 T38 K39 L40 S45 H46 T47 A49 A50 Q51 G52 G53 Y166 F167 A168 A202 T203 G204 D222 L253 H354 Y355 G386 E387 A401 S403 L404 L407
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): F130 Q251 H253 L263 E266 R269 R297 H364 Y365 R408
• Catalytic site (residue number reindexed from 1): F120 Q241 H243 L253 E256 R259 R287 H354 Y355 R398
• Enzyme Commision number: 1.3.5.1: succinate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0008177 succinate dehydrogenase (quinone) activity
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0006099 tricarboxylic acid cycle
• GO:0006105 succinate metabolic process
• GO:0006121 mitochondrial electron transport, succinate to ubiquinone
• GO:0022900 electron transport chain
• GO:0022904 respiratory electron transport chain

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0045273 respiratory chain complex II (succinate dehydrogenase)

External links

• PDB: RCSB:6myu, PDBe:6myu, PDBj:6myu
• PDBsum: 6myu
• PubMed: 34089891
• UniProt: Q9YHT1|SDHA_CHICK Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (Gene Name=SDHA)