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(-) Description

Title :  CRYSTAL STRUCTURE OF A METABOLIC REDUCTASE WITH (E)-1-BENZYL-5-((1-METHYL-5-OXO-2-THIOXOIMIDAZOLIDIN-4-YLIDENE)METHYL)PYRIDIN-2(1H)-ONE
 
Authors :  B. Zheng, F. Wu, H. Jiang, M. Kogiso, Y. Yao, C. Zhou, X. Li, Y. Song
Date :  21 Jan 15  (Deposition) - 27 Jul 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.29
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase/Oxidoreductase Inhibitor, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Wu, H. Jiang, B. Zheng, M. Kogiso, Y. Yao, C. Zhou, X. N. Li, Y. Song
Inhibition Of Cancer-Associated Mutant Isocitrate Dehydrogenases By 2-Thiohydantoin Compounds.
J. Med. Chem. V. 58 6899 2015
PubMed-ID: 26280302  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00684

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
    Chains: A, B
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-KG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
142W2Ligand/Ion(E)-1-BENZYL-5-((1-METHYL-5-OXO-2-THIOXOIMIDAZOLIDIN-4-YLIDENE)METHYL)PYRIDIN-2(1H)-ONE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:77 , SER A:94 , ARG A:100 , ASN A:101 , NAP A:502binding site for residue 42W A 501
2AC2SOFTWARETHR A:75 , THR A:77 , ARG A:82 , HIS A:309 , GLY A:310 , THR A:311 , THR A:313 , ARG A:314 , HIS A:315 , 42W A:501 , ALA B:256 , LYS B:260binding site for residue NAP A 502
3AC3SOFTWARETHR B:77 , LYS B:93 , SER B:94 , GLY B:97 , ARG B:100binding site for residue 42W B 501
4AC4SOFTWARELYS B:72 , ALA B:74 , THR B:75 , THR B:77 , ASN B:96 , GLY B:289 , GLU B:306 , HIS B:309 , GLY B:310 , THR B:311 , VAL B:312 , THR B:313 , ARG B:314 , HIS B:315 , THR B:327 , ASN B:328binding site for residue NAP B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XS3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XS3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XS3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XS3)

(-) Exons   (0, 0)

(no "Exon" information available for 4XS3)

(-) 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:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee..........eeeee....eeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh..hhhhhh....eeeeehhhhhhhhh.....eeeee.hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xs3 A   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRKPIIIGHHYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQA 412
                                    12        22        32        42        52        62        72        82        92       102       112      |128    || 143       153       163       173       183       193       203       213       223       233       243       253       263      |289       299       309       319       329       339       349       359       369       379       389       399       409   
                                                                                                                                              119|    133|                                                                                                                                270|                                                                                                                             
                                                                                                                                               126     139                                                                                                                                 287                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.........eeeeeee..eee.....eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhh...eeeeee.hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xs3 B   4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRVKPIIIGHHATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAK 413
                                    13        23        33        43        53        63        73        83        93       103       113     ||128    || 145       155       165       175       185       195       205       215       225       235       245       255       265   ||  292       302       312       322       332       342       352       362       372       382       392       402       412 
                                                                                                                                             119|     133|                                                                                                                             269|                                                                                                                              
                                                                                                                                              125      141                                                                                                                              287
   Legend:   → Mismatch (orange background)
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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 4XS3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XS3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XS3)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)

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  4xs3
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  1.1.1.42
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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 5de1 5gir 5k10 5k11 5l57 5l58 5lge 5sun 5svf 5tqh

(-) Related Entries Specified in the PDB File

4xrx