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(-) Description

Title :  COMPLEX OF MITOCHONDRIAL ISOCITRATE DEHYDROGENASE R140Q MUTANT WITH AGI-6780 INHIBITOR
 
Authors :  W. Wei, L. Chen, M. Wu, F. Jiang, J. Travins, K. Qian, B. Delabarre
Date :  18 Feb 13  (Deposition) - 10 Apr 13  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Inhibitor Complex, Metabolic Enzyme Oncometabolite, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Wang, J. Travins, B. Delabarre, V. Penard-Lacronique, S. Schalm, E. Hansen, K. Straley, A. Kernytsky, W. Liu, C. Gliser, H. Yang, S. Gross, E. Artin, V. Saada, E. Mylonas, C. Quivoron, J. Popovici-Muller, J. O. Saunders, F. G. Salituro, S. Yan, S. Murray, W. Wei, Y. Gao, L. Dang, M. Dorsch, S. Agresta, D. P. Schenkein, S. A. Biller, S. M. Su, S. De Botton, K. E. Yen
Targeted Inhibition Of Mutant Idh2 In Leukemia Cells Induce Cellular Differentiation.
Science V. 340 622 2013
PubMed-ID: 23558173  |  Reference-DOI: 10.1126/SCIENCE.1234769

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL
    Chains: A, B
    EC Number: 1.1.1.42
    Engineered: YES
    Fragment: UNP RESIDUES 41-452
    Gene: IDH2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IDH, ICD-M, IDP, NADP(+)-SPECIFIC ICDH, OXALOSUCCINATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
11K91Ligand/Ion1-[5-(CYCLOPROPYLSULFAMOYL)-2-THIOPHEN-3-YL-PHENYL]-3-[3-(TRIFLUOROMETHYL)PHENYL]UREA
2CA2Ligand/IonCALCIUM ION
3GOL4Ligand/IonGLYCEROL
4NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:112 , ALA A:114 , THR A:115 , ILE A:116 , THR A:117 , ARG A:122 , ASN A:136 , GLU A:345 , HIS A:348 , GLY A:349 , THR A:350 , VAL A:351 , THR A:352 , ARG A:353 , HIS A:354 , ASN A:367 , GOL A:505 , HOH A:608 , HOH A:642 , HOH A:659 , HOH A:668 , HOH A:686 , HOH A:692 , HOH A:784 , HOH A:874 , HOH A:980BINDING SITE FOR RESIDUE NDP A 501
2AC2SOFTWARETRP A:164 , VAL A:294 , VAL A:297 , LEU A:298 , TRP A:306 , TYR A:311 , ASP A:312 , VAL A:315 , GLN A:316 , ILE A:319 , LEU A:320 , TRP B:164 , VAL B:294 , VAL B:297 , LEU B:298 , TRP B:306 , TYR B:311 , ASP B:312 , VAL B:315 , GLN B:316 , ILE B:319 , LEU B:320BINDING SITE FOR RESIDUE 1K9 A 502
3AC3SOFTWAREASP A:314 , ASP A:318 , HOH A:871 , ASP B:291 , HOH B:601 , HOH B:602BINDING SITE FOR RESIDUE CA A 503
4AC4SOFTWAREASP A:271 , LYS A:272 , HIS A:273 , TYR A:274 , LYS A:275 , THR A:276 , HOH A:799BINDING SITE FOR RESIDUE GOL A 504
5AC5SOFTWARETHR A:117 , SER A:134 , ASN A:136 , NDP A:501BINDING SITE FOR RESIDUE GOL A 505
6AC6SOFTWAREVAL A:185 , ALA A:186 , ASP A:187 , ARG A:188 , HOH A:954 , PHE B:196 , LYS B:205 , HOH B:735BINDING SITE FOR RESIDUE GOL A 506
7AC7SOFTWARELYS A:280 , LYS A:282 , GLU A:404 , ASN A:444 , HOH A:660 , HOH A:739 , HOH A:830 , HOH A:1019BINDING SITE FOR RESIDUE GOL A 507
8AC8SOFTWARELYS B:112 , ALA B:114 , THR B:115 , THR B:117 , ARG B:122 , ASN B:136 , LEU B:327 , GLU B:345 , HIS B:348 , GLY B:349 , THR B:350 , VAL B:351 , THR B:352 , ARG B:353 , HIS B:354 , ASN B:367 , HOH B:673 , HOH B:685 , HOH B:704 , HOH B:765 , HOH B:781 , HOH B:800 , HOH B:839 , HOH B:864BINDING SITE FOR RESIDUE NDP B 501
9AC9SOFTWAREASP A:291 , HOH A:601 , ASP B:314 , ASP B:318 , HOH B:603 , HOH B:819 , HOH B:847BINDING SITE FOR RESIDUE CA B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JA8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JA8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JA8)

(-) Exons   (0, 0)

(no "Exon" information available for 4JA8)

(-) Sequences/Alignments

Asymmetric/Biological 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:416
                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4ja8a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeeee.hhhhhhhhhhhhhhh....ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeee...hhhhhheeeee...eeeeeeeee......eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh.hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ja8 A  41 DKRIKVAKPVVEMDGDEMTRIIWQFIKEKLILPHVDIQLKYFDLGLPNRDQTDDQVTIDSALATQKYSVAVKCATITPDEARVEEFKLKKMWKSPNGTIQNILGGTVFREPIICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVADRAGTFKMVFTPKDGSGVKEWEVYNFPAGGVGMGMYNTDESISGFAHSCFQYAIQKKWPLYMSTKNTILKAYDGRFKDIFQEIFDKHYKTDFDKNKIWYEHRLIDDMVAQVLKSSGGFVWACKNYDGDVQSDILAQGFGSLGLMTSVLVCPDGKTIEAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLIRFAQMLEKVCVETVESGAMTKDLAGCIHGLSNVKLNEHFLNTTDFLDTIKSNLDRALGRQHHHH 456
                                    50        60        70        80        90       100       110       120       130       140       150       160       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       420       430       440       450      


Chain B from PDB  Type:PROTEIN  Length:406
                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4ja8b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....eeeee.hhhhhhhhhhhhhhhhhh.ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeee...hhhhhheeeee...eeeeeeeee......eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh.hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ja8 B  43 RIKVAKPVVEMDGDEMTRIIWQFIKEKLILPHVDIQLKYFDLGLPNRDQTDDQVTIDSALATQKYSVAVKCATITPDEARVEEFKLKKMWKSPNGTIQNILGGTVFREPIICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVADRAGTFKMVFTPKDGSGVKEWEVYNFPAGGVGMGMYNTDESISGFAHSCFQYAIQKKWPLYMSTKNTILKAYDGRFKDIFQEIFDKHYKTDFDKNKIWYEHRLIDDMVAQVLKSSGGFVWACKNYDGDVQSDILAQGFGSLGLMTSVLVCPDGKTIEAEAAHGTVTRHYREHQKGRPTSTNPIASIFAWTRGLEHRGKLDGNQDLIRFAQMLEKVCVETVESGAMTKDLAGCIHGLSNVKLNEHFLNTTDFLDTIKSNLDRA 448
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JA8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JA8)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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  4ja8
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 Related Entries

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        IDHP_HUMAN | P48735: 5gis 5i95 5i96 5svn 5svo

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