PDB entry 6bky

View 6bky on RCSB PDB site
Description: Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with Cmpd2
Class: OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor
Keywords: dehydrogenase, inhibitor, OXIDOREDUCTASE, OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Deposited on 2017-11-09, released 2018-07-25
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-07-25, with a file datestamp of 2018-07-20.
Experiment type: XRAY
Resolution: 2.17 Å
R-factor: N/A
AEROSPACI score: 0.27 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: isocitrate dehydrogenase [nadp] cytoplasmic
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH1, PICD
    Database cross-references and differences (RAF-indexed):
    • Uniprot O75874 (Start-413)
      • expression tag (414-417)
    Domains in SCOPe 2.07: d6bkya1, d6bkya2
  • Chain 'B':
    Compound: isocitrate dehydrogenase [nadp] cytoplasmic
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH1, PICD
    Database cross-references and differences (RAF-indexed):
    • Uniprot O75874 (Start-413)
      • expression tag (414)
    Domains in SCOPe 2.07: d6bkyb1, d6bkyb2
  • Chain 'C':
    Compound: isocitrate dehydrogenase [nadp] cytoplasmic
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH1, PICD
    Database cross-references and differences (RAF-indexed):
    • Uniprot O75874 (Start-413)
      • expression tag (414-415)
    Domains in SCOPe 2.07: d6bkyc1, d6bkyc2
  • Chain 'D':
    Compound: isocitrate dehydrogenase [nadp] cytoplasmic
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH1, PICD
    Database cross-references and differences (RAF-indexed):
    • Uniprot O75874 (Start-413)
      • expression tag (414-417)
    Domains in SCOPe 2.07: d6bkyd1, d6bkyd2
  • Chain 'E':
    Compound: isocitrate dehydrogenase [nadp] cytoplasmic
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH1, PICD
    Database cross-references and differences (RAF-indexed):
    • Uniprot O75874 (Start-413)
      • expression tag (414-417)
    Domains in SCOPe 2.07: d6bkye1, d6bkye2
  • Chain 'F':
    Compound: isocitrate dehydrogenase [nadp] cytoplasmic
    Species: Homo sapiens [TaxId:9606]
    Gene: IDH1, PICD
    Database cross-references and differences (RAF-indexed):
    • Uniprot O75874 (Start-413)
      • expression tag (414)
    Domains in SCOPe 2.07: d6bkyf1, d6bkyf2
  • Heterogens: K32, LMR, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6bkyA (A:)
    mskkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkda
    aeaikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprl
    vsgwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvam
    gmynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfe
    aqkiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdg
    ktveaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanale
    evsietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqaklslehhh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6bkyA (A:)
    kkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkdaae
    aikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprlvs
    gwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvamgm
    ynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfeaq
    kiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdgkt
    veaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanaleev
    sietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqaklsleh
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6bkyB (B:)
    mskkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkda
    aeaikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprl
    vsgwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvam
    gmynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfe
    aqkiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdg
    ktveaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanale
    evsietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqaklslehhh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6bkyB (B:)
    kkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkdaae
    aikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprlvs
    gwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvamgm
    ynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfeaq
    kiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdgkt
    veaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanaleev
    sietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqakls
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6bkyC (C:)
    mskkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkda
    aeaikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprl
    vsgwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvam
    gmynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfe
    aqkiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdg
    ktveaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanale
    evsietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqaklslehhh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6bkyC (C:)
    kkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkdaae
    aikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprlvs
    gwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvamgm
    ynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfeaq
    kiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdgkt
    veaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanaleev
    sietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqaklsl
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6bkyD (D:)
    mskkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkda
    aeaikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprl
    vsgwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvam
    gmynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfe
    aqkiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdg
    ktveaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanale
    evsietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqaklslehhh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6bkyD (D:)
    kkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkdaae
    aikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprlvs
    gwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvamgm
    ynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfeaq
    kiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdgkt
    veaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanaleev
    sietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqaklsleh
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >6bkyE (E:)
    mskkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkda
    aeaikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprl
    vsgwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvam
    gmynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfe
    aqkiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdg
    ktveaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanale
    evsietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqaklslehhh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6bkyE (E:)
    kkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkdaae
    aikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprlvs
    gwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvamgm
    ynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfeaq
    kiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdgkt
    veaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanaleev
    sietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqaklsleh
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >6bkyF (F:)
    mskkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkda
    aeaikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprl
    vsgwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvam
    gmynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfe
    aqkiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdg
    ktveaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanale
    evsietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqaklslehhh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6bkyF (F:)
    kkisggsvvemqgdemtriiwelikeklifpyveldlhsydlgienrdatndqvtkdaae
    aikkhnvgvkcatitpdekrveefklkqmwkspngtirnilggtvfreaiickniprlvs
    gwvkpiiigrhaygdqyratdfvvpgpgkveitytpsdgtqkvtylvhnfeegggvamgm
    ynqdksiedfahssfqmalskgwplylstkntilkkydgrfkdifqeiydkqyksqfeaq
    kiwyehrliddmvaqamkseggfiwacknydgdvqsdsvaqgygslgmmtsvlvcpdgkt
    veaeaahgtvtrhyrmyqkgqetstnpiasifawtrglahrakldnnkelaffanaleev
    sietieagfmtkdlaacikglpnvqrsdylntfefmdklgenlkiklaqakls