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(-) Description

Title :  IDH1 R132H IN COMPLEX WITH IDH125
 
Authors :  X. Xie, R. Kulathila
Date :  05 Aug 16  (Deposition) - 08 Feb 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Isocitrate Dehydrogenase, Rossmann Fold, Nadph, Inhibitor, 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, C, B, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
170P4Ligand/Ion(4S)-3-(2-{[(1S)-1-PHENYLETHYL]AMINO}PYRIMIDIN-4-YL)-4-(PROPAN-2-YL)-1,3-OXAZOLIDIN-2-ONE
2FLC4Ligand/IonCITRATE ANION
3NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
170P2Ligand/Ion(4S)-3-(2-{[(1S)-1-PHENYLETHYL]AMINO}PYRIMIDIN-4-YL)-4-(PROPAN-2-YL)-1,3-OXAZOLIDIN-2-ONE
2FLC2Ligand/IonCITRATE ANION
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
170P2Ligand/Ion(4S)-3-(2-{[(1S)-1-PHENYLETHYL]AMINO}PYRIMIDIN-4-YL)-4-(PROPAN-2-YL)-1,3-OXAZOLIDIN-2-ONE
2FLC2Ligand/IonCITRATE ANION
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
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 , 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 , FLC A:503 , HOH A:614 , HOH A:630 , HOH A:686binding site for residue NDP A 501
02AC2SOFTWAREARG A:109 , ALA A:111 , ARG A:119 , LEU A:120 , TRP A:124 , PRO A:127 , ILE A:128 , ILE A:130 , SER A:278 , ALA A:282 , TYR A:285 , SER A:287binding site for residue 70P A 502
03AC3SOFTWARETHR A:77 , SER A:94 , ASN A:96 , ARG A:100 , NDP A:501binding site for residue FLC A 503
04AC4SOFTWARELYS C:72 , ALA C:74 , THR C:75 , ILE C:76 , THR C:77 , ARG C:82 , ASN C:96 , GLU C:306 , HIS C:309 , GLY C:310 , THR C:311 , VAL C:312 , THR C:313 , ARG C:314 , HIS C:315 , THR C:327 , ASN C:328 , FLC C:503 , HOH C:649binding site for residue NDP C 501
05AC5SOFTWAREARG C:109 , ALA C:111 , ARG C:119 , LEU C:120 , TRP C:124 , ILE C:128 , ALA C:282 , TYR C:285 , SER C:287binding site for residue 70P C 502
06AC6SOFTWARETHR C:77 , SER C:94 , NDP C:501binding site for residue FLC C 503
07AC7SOFTWARELYS B:72 , ALA B:74 , THR B:75 , THR B:77 , ARG B:82 , ASN B:96 , GLN B:283 , LEU B:288 , 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 , FLC B:503 , HOH B:627 , HOH B:650 , HOH B:684 , HOH B:710 , HOH B:720 , LYS D:260binding site for residue NDP B 501
08AC8SOFTWAREARG B:109 , ALA B:111 , ILE B:113 , ARG B:119 , LEU B:120 , TRP B:124 , ILE B:128 , ILE B:130 , VAL B:281 , ALA B:282 , TYR B:285 , SER B:287 , MET B:291binding site for residue 70P B 502
09AC9SOFTWARETHR B:77 , SER B:94 , ASN B:96 , ARG B:100 , NDP B:501binding site for residue FLC B 503
10AD1SOFTWARELYS D:72 , ALA D:74 , THR D:75 , THR D:77 , ARG D:82 , ASN D:96 , GLU D:306 , 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 , FLC D:503 , HOH D:616binding site for residue NDP D 501
11AD2SOFTWAREARG D:109 , ALA D:111 , ILE D:113 , ARG D:119 , LEU D:120 , TRP D:124 , PRO D:127 , ILE D:128 , ILE D:130 , ALA D:282 , TYR D:285 , SER D:287 , MET D:291binding site for residue 70P D 502
12AD3SOFTWARETHR D:77 , SER D:94 , ASN D:96 , ARG D:100 , NDP D:501binding site for residue FLC D 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5SVF)

(-) 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:398
                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeee...eeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeee...hhhhhhhhhhhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5svf A   4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQA 412
                                    13        23        33        43        53        63        73        83        93       103       113       123       133||     149       159       169       179       189       199       209       219       229       239       249       259       269 ||    284       294       304       314       324       334       344       354       364       374       384       394       404        
                                                                                                                                                            134|                                                                                                                               271|                                                                                                                                       
                                                                                                                                                             141                                                                                                                                277                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.................eeee...eeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh....eeee..hhhhhhhhhhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5svf B   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQA 412
                                    12        22        32        42        52        62        72        82        92       102       112       122       132||     148       158       168       178       188       198       208       218       228       238       248       258       268 ||    285       295       305       315       325       335       345       355       365       375       385       395       405       
                                                                                                                                                            133|                                                                                                                               270|                                                                                                                                      
                                                                                                                                                             140                                                                                                                                278                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhh..hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee.................eeee....eeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhh....eeee..hhhhhhhhhhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5svf C   4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHARATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL 414
                                    13        23        33        43        53        63        73        83        93       103       113       123       133||     148       158       168       178       188       198       208       218       228       238       248       258       268 ||    285       295       305       315       325       335       345       355       365       375       385       395       405         
                                                                                                                                                            134|                                                                                                                               270|                                                                                                                                        
                                                                                                                                                             140                                                                                                                                278                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:402
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeee...hhhhhheeeee...eeeeeeeee......eeeeeeee....eeeeeeeeehhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeee...hhhhhhhhhhhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5svf D   4 KISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLA 410
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       278       288       298       308       318       328       338       348       358       368       378       388       398       408  
                                                                                                                                                                                                                                                                                                     271|                                                                                                                                     
                                                                                                                                                                                                                                                                                                      277
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  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 5SVF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 30)

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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 5lge 5sun 5tqh

(-) Related Entries Specified in the PDB File

5sun 5SUN CONTAINS A DIFFERENT ISOFORM OF THE PROTEIN
5svn
5svo