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(-) Description

Title :  IDH1 R132H IN COMPLEX WITH IDH146
 
Authors :  X. Xie, R. Kulathila
Date :  03 Aug 16  (Deposition) - 08 Feb 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor, Isocitrate Dehydrogenase, Nadph, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Xie, D. Baird, K. Bowen, V. Capka, J. Chen, G. Chenail, Y. Cho, J. Dooley, A. Farsidjani, P. Fortin, D. Kohls, R. Kulathila, F. Lin, D. Mckay, L. Rodrigues, D. Sage, B. B. Toure, S. Van Der Plas, K. Wright, M. Xu, H. Yin, J. Levell, R. A. Pagliarini
Allosteric Mutant Idh1 Inhibitors Reveal Mechanisms For Idh Mutant And Isoform Selectivity.
Structure V. 25 506 2017
PubMed-ID: 28132785  |  Reference-DOI: 10.1016/J.STR.2016.12.017

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
    Chains: A, B
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
170Q2Ligand/Ion3-BENZYL-N-[3-(DIMETHYLSULFAMOYL)PHENYL]-4-OXO-3,4-DIHYDROPHTHALAZINE-1-CARBOXAMIDE
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
5SO44Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:72 , THR A:75 , ILE A:76 , THR A:77 , ARG A:82 , ASN A:96 , GLU A:306 , HIS A:309 , GLY A:310 , THR A:311 , VAL A:312 , THR A:313 , ARG A:314 , HIS A:315 , THR A:327 , ASN A:328 , HOH A:619binding site for residue NDP A 501
02AC2SOFTWAREARG A:109 , ALA A:111 , TRP A:124 , LYS A:126 , ILE A:128 , ILE A:130 , ALA A:258 , GLY A:263 , TRP A:267 , 70Q B:502binding site for residue 70Q A 502
03AC3SOFTWAREHIS A:170 , PHE A:172 , GLU A:173 , GLU A:174 , GLN B:185binding site for residue SO4 A 503
04AC4SOFTWAREGLU A:324 , THR A:325 , ASN A:393 , PHE A:395binding site for residue SO4 A 504
05AC5SOFTWARELYS A:374 , HOH A:608binding site for residue EDO A 505
06AC6SOFTWARETHR A:77 , SER A:94 , ASN A:96binding site for residue DMS A 506
07AC7SOFTWARELYS A:260 , LYS B:72 , THR B:75 , THR B:77 , ARG B:82 , ASN B:96 , 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:328 , HOH B:601 , HOH B:606 , HOH B:612binding site for residue NDP B 501
08AC8SOFTWARE70Q A:502 , ARG B:109 , ILE B:113 , TRP B:124 , LYS B:126 , ILE B:128 , VAL B:255 , ALA B:258 , MET B:259 , GLY B:263binding site for residue 70Q B 502
09AC9SOFTWAREGLN A:185 , HIS B:170 , PHE B:172 , GLU B:173 , GLU B:174binding site for residue SO4 B 503
10AD1SOFTWARELYS B:151 , GLU B:153 , GLY B:161 , GLN B:163binding site for residue SO4 B 504
11AD2SOFTWAREGLN A:411 , TYR B:319 , GLY B:322 , GLN B:323binding site for residue EDO B 505
12AD3SOFTWARETHR B:77 , SER B:94 , ASN B:96 , HOH B:602binding site for residue DMS B 506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5SUN)

(-) 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:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.................eee..eeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhh.....eeee..hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5sun A   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAK 413
                                    12        22        32        42        52        62        72        82        92       102       112       122       132|      150       160       170       180       190       200       210       220       230       240       250       260       270||     295       305       315       325       335       345       355       365       375       385       395       405        
                                                                                                                                                           132|                                                                                                                               271|                                                                                                                              
                                                                                                                                                            141                                                                                                                                287                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhh.......hhhhhhhhhhh.eeeeee.................eeeee..eeeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh.....eeee..hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5sun B   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHARATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQA 412
                                    12        22        32        42        52        62        72        82        92       102       112       122       132 ||    147       157       167       177       187       197       207       217       227       237       247       257       267   ||  292       302       312       322       332       342       352       362       372       382       392       402       412
                                                                                                                                                             134|                                                                                                                                271|                                                                                                                             
                                                                                                                                                              140                                                                                                                                 287
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)

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  5sun
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  IDHC_HUMAN | O75874
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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 4xs3 5de1 5gir 5k10 5k11 5l57 5l58 5lge 5svf 5tqh

(-) Related Entries Specified in the PDB File

5svf 5svn 5svo