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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN IDH1 MUTANT (R132H) IN COMPLEX WITH NADP+ AND AN INHIBITOR RELATED TO BAY 1436032
 
Authors :  R. C. Hillig, U. Hars, I. P. Korndoerfer
Date :  07 Jul 16  (Deposition) - 08 Feb 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Idh1, Allosteric Inhibitor, Nadp+, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pusch, S. Krausert, V. Fischer, J. Balss, M. Ott, D. Schrimpf, D. Capper, F. Sahm, J. Eisel, A. C. Beck, M. Jugold, V. Eichwald, S. Kaulfuss, O. Panknin, H. Rehwinkel, K. Zimmermann, R. C. Hillig, J. Guenther, L. Toschi, R. Neuhaus, A. Haegebart, H. Hess-Stumpp, M. Bauser, W. Wick, A. Unterberg, C. Herold-Mende, M. Platten, A. Von Deimling
Pan-Mutant Idh1 Inhibitor Bay 1436032 For Effective Treatment Of Idh1 Mutant Astrocytoma In Vivo.
Acta Neuropathol. V. 133 629 2017
PubMed-ID: 28124097  |  Reference-DOI: 10.1007/S00401-017-1677-Y

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
    Chains: A, B, C, D
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P10T7-2
    Expression System Taxid: 562
    Expression System Variant: RIL
    Gene: IDH1, PICD
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IDH,CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE,IDP,NADP(+)- SPECIFIC ICDH,OXALOSUCCINATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
16VN2Ligand/Ion2-[(4-PROPAN-2-YLPHENYL)AMINO]-1-[(1~{S},5~{S})-3,3,5-TRIMETHYLCYCLOHEXYL]BENZIMIDAZOLE-5-CARBOXYLIC ACID
2ACT1Ligand/IonACETATE ION
3EDO3Ligand/Ion1,2-ETHANEDIOL
4NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
16VN1Ligand/Ion2-[(4-PROPAN-2-YLPHENYL)AMINO]-1-[(1~{S},5~{S})-3,3,5-TRIMETHYLCYCLOHEXYL]BENZIMIDAZOLE-5-CARBOXYLIC ACID
2ACT-1Ligand/IonACETATE ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
4NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
16VN1Ligand/Ion2-[(4-PROPAN-2-YLPHENYL)AMINO]-1-[(1~{S},5~{S})-3,3,5-TRIMETHYLCYCLOHEXYL]BENZIMIDAZOLE-5-CARBOXYLIC ACID
2ACT1Ligand/IonACETATE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:72 , ALA A:74 , THR A:75 , THR A:77 , ARG A:82 , ASN A:96 , LEU A:288 , GLU A:306 , ALA A:307 , HIS A:309 , GLY A:310 , THR A:311 , VAL A:312 , THR A:313 , ARG A:314 , HIS A:315 , ASN A:328 , HOH A:620 , HOH A:627 , HOH A:645 , HOH A:661 , HOH A:678 , HOH A:705binding site for residue NAP A 501
02AC2SOFTWAREGLU A:247 , HOH A:615 , HOH A:617binding site for residue EDO A 502
03AC3SOFTWARELYS B:72 , ALA B:74 , THR B:75 , THR B:77 , ARG B:82 , ASN B:96 , GLN B:277 , ASP B:279 , LEU B:288 , GLU B:306 , ALA B:307 , HIS B:309 , GLY B:310 , THR B:311 , VAL B:312 , THR B:313 , ARG B:314 , HIS B:315 , ASN B:328 , HOH B:603 , HOH B:611 , HOH B:619 , HOH B:641 , HOH B:650 , HOH B:683 , HOH B:693binding site for residue NAP B 501
04AC4SOFTWARELEU A:120 , MET A:259 , VAL A:276 , GLN A:277 , SER A:280 , VAL A:281 , TRP B:124 , ILE B:128 , ILE B:130 , HIS B:132 , CYS B:269 , SER B:280 , VAL B:281binding site for residue 6VN B 502
05AC5SOFTWARELYS C:72 , ALA C:74 , THR C:75 , THR C:77 , ARG C:82 , ASN C:96 , LEU C:288 , GLU C:306 , ALA C:307 , HIS C:309 , GLY C:310 , THR C:311 , VAL C:312 , THR C:313 , ARG C:314 , HIS C:315 , ASN C:328 , HOH C:605 , HOH C:611 , HOH C:613 , HOH C:620 , HOH C:646 , HOH C:651 , HOH C:670 , HOH C:713binding site for residue NAP C 501
06AC6SOFTWAREGLY C:370 , HOH C:612 , HOH C:680binding site for residue EDO C 502
07AC7SOFTWAREHOH C:679binding site for residue EDO C 503
08AC8SOFTWARELYS D:72 , ALA D:74 , THR D:75 , THR D:77 , ARG D:82 , ASN D:96 , GLN D:277 , LEU D:288 , GLU D:306 , ALA D:307 , HIS D:309 , GLY D:310 , THR D:311 , VAL D:312 , THR D:313 , ARG D:314 , HIS D:315 , THR D:327 , ASN D:328 , HOH D:604 , HOH D:610 , HOH D:613 , HOH D:629 , HOH D:650 , HOH D:661binding site for residue NAP D 501
09AC9SOFTWAREGLU C:47 , ASP C:50 , HOH C:603 , HOH C:641 , ASP D:50 , LYS D:89binding site for residue ACT D 502
10AD1SOFTWARELEU C:120 , MET C:259 , VAL C:276 , GLN C:277 , SER C:280 , VAL C:281 , HOH C:627 , TRP D:124 , ILE D:130 , HIS D:132 , CYS D:269 , SER D:280 , VAL D:281 , TYR D:285 , HOH D:621binding site for residue 6VN D 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LGE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LGE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LGE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LGE)

(-) Exons   (0, 0)

(no "Exon" information available for 5LGE)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:406
                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.................eeee......eeeeeeee.....eeeeee...........eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh.....eeee.......hhhhhh....hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lge A   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKVEITYTPTYLHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKLSL 416
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     ||170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410      
                                                                                                                                                                                     158| ||                                                                                                                                                                                                                                                      
                                                                                                                                                                                      166 ||                                                                                                                                                                                                                                                      
                                                                                                                                                                                        168|                                                                                                                                                                                                                                                      
                                                                                                                                                                                         170                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:407
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.................eeee......eeeeeeee....eeeeee..eeeee......eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh.....eeee..........hhhhh..hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lge B   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKVEITYTVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKLSL 416
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152    || 169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       
                                                                                                                                                                                    157|                                                                                                                                                                                                                                                           
                                                                                                                                                                                     165                                                                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.................eeee......eeeeeeee.....eeeee........eeeeee......eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh.....eeee......hhhhhh....hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lge C   2 SKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKLSL 416
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  ||   282       292       302       312       322       332       342       352       362       372       382       392       402       412    
                                                                                                                                                                                                                                                                                                          274|                                                                                                                                            
                                                                                                                                                                                                                                                                                                           276                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:412
                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.................eeee......eeeeeeee.....eeeee........eeeeee......eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh.....eeee.........hhhhh..hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lge D   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKLS 415
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272||     283       293       303       313       323       333       343       353       363       373       383       393       403       413  
                                                                                                                                                                                                                                                                                                        273|                                                                                                                                            
                                                                                                                                                                                                                                                                                                         275
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5LGE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LGE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LGE)

(-) Gene Ontology  (30, 30)

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  5lge
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  IDHC_HUMAN | O75874
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IDHC_HUMAN | O75874: 1t09 1t0l 3inm 3map 3mar 3mas 4i3k 4i3l 4kzo 4l03 4l04 4l06 4umx 4umy 4xrx 4xs3 5de1 5gir 5k10 5k11 5l57 5l58 5sun 5svf 5tqh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LGE)