Structure of PDB 6vax Chain C Binding Site BS01

Receptor Information

>6vax Chain C (length=611) Species: 9606 (Homo sapiens)

QYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAA
QGGINAALGNMEEDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPAAVVEL
ENYGMPFSRTEDGKIYQRAFGGQSLKFGKGGQAHRCCCVADRTGHSLLHT
LYGRSLRYDTSYFVEYFALDLLMENGECRGVIALCIEDGSIHRIRAKNTV
VATGGYGRTYFSCTSAHTSTGDGTAMITRAGLPCQDLEFVQFHPTGIYGA
GCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTLEIRE
GRGCGPEKDHVYLQLHHLPPEQLATRLPGISETAMIFAGVDVTKEPIPVL
PTVHYNMGGIPTNYKGQVLRHVNGQDQIVPGLYACGEAACASVHGANRLG
ANSLLDLVVFGRACALSIEESCRPGDKVPPIKPNAGEESVMNLDKLRFAD
GSIRTSELRLSMQKSMQNHAAVFRVGSVLQEGCGKISKLYGDLKHLKTFD
RGMVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDYKVRIDE
YDYSKPIQGQQKKPFEEHWRKHTLSYVDVGTGKVTLEYRPVIDKTLNEAD
CATVPPAIRSY

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: 6vax Chain C Residue 702

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vax The roles of SDHAF2 and dicarboxylate in covalent flavinylation of SDHA, the human complex II flavoprotein.
• Resolution: 2.59 Å
• Binding residue (original residue number in PDB): G68 A69 G70 T91 K92 L93 S98 H99 T100 A103 G105 A221 A255 T256 G257 T267 D275 H407 Y408 E440 A454 S456 L457 L460
• Binding residue (residue number reindexed from 1): G15 A16 G17 T38 K39 L40 S45 H46 T47 A50 G52 A168 A202 T203 G204 T214 D222 H354 Y355 E387 A401 S403 L404 L407
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): F173 Q294 H296 L306 E309 R312 R340 H407 Y408 R451
• 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:0005515 protein binding
• 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:0007399 nervous system development
• GO:0022900 electron transport chain
• GO:0022904 respiratory electron transport chain
• GO:0042776 proton motive force-driven mitochondrial ATP synthesis

Cellular Component

• GO:0005730 nucleolus
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005759 mitochondrial matrix
• GO:0045273 respiratory chain complex II (succinate dehydrogenase)

External links

• PDB: RCSB:6vax, PDBe:6vax, PDBj:6vax
• PDBsum: 6vax
• PubMed: 32887801
• UniProt: P31040|SDHA_HUMAN Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (Gene Name=SDHA)