Structure of PDB 1yq3 Chain A Binding Site BS01

Receptor Information

>1yq3 Chain A (length=614) Species: 9031 (Gallus gallus)

ISTQYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHT
VAAQGGINAALGNMEDDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPAAV
IELENYGMPFSRTEEGKIYQRAFGGQSLQFGKGGQAHRCCCVADRTGHSL
LHTLYGRSLRYDTSYFVEYFALDLLMENGECRGVIALCIEDGTIHRFRAK
NTVIATGGYGRTYFSCTSAHTSTGDGTAMVTRAGLPCQDLEFVQFHPTGI
YGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTIE
IREGRGCGPEKDHVYLQLHHLPPQQLATRLPGISETAMIFAGVDVTKEPI
PVLPTVHYNMGGIPTNYKGQVITHVNGEDKVVPGLYACGEAASASVHGAN
RLGANSLLDLVVFGRACALTIAETCKPGEPVPSIKPNAGEESVANLDKLR
FADGTIRTSEARLNMQKTMQSHAAVFRTGSILQEGCEKLSQIYRDLAHLK
TFDRGIVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDYKLR
IDEFDYSKPLQGQQKRPFEEHWRKHTLSYVDVKSGKVTLKYRPVIDRTLN
EEDCSSVPPAIRSY

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: 1yq3 Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1yq3 3-Nitropropionic Acid Is a Suicide Inhibitor of Mitochondrial Respiration That, upon Oxidation by Complex II, Forms a Covalent Adduct with a Catalytic Base Arginine in the Active Site of the Enzyme
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): G25 A26 G27 A29 V47 T48 K49 L50 S55 H56 T57 A59 A60 Q61 G62 G63 F177 A178 T213 D232 L263 H364 Y365 E397 A411 S413 L414 L417
• Binding residue (residue number reindexed from 1): G18 A19 G20 A22 V40 T41 K42 L43 S48 H49 T50 A52 A53 Q54 G55 G56 F170 A171 T206 D225 L256 H357 Y358 E390 A404 S406 L407 L410
• 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): F123 Q244 H246 L256 E259 R262 R290 H357 Y358 R401
• 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:1yq3, PDBe:1yq3, PDBj:1yq3
• PDBsum: 1yq3
• PubMed: 16371358
• UniProt: Q9YHT1|SDHA_CHICK Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (Gene Name=SDHA)