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(-) Description

Title :  CRYSTAL STRUCTURE OF ISO-CITRATE DEHYDROGENASE R132H IN COMPLEX WITH A NOVEL INHIBITOR (COMPOUND 13A)
 
Authors :  C. Levy
Date :  28 May 16  (Deposition) - 14 Dec 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  R132H, Iso-Citrate Dehydrogenase, Allosteric, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Jones, J. Ahmet, K. Ayton, M. Ball, M. Cockerill, E. Fairweather, N. Hamilton, P. Harper, J. Hitchin, A. Jordan, C. Levy, R. Lopez, E. Mckenzie, M. Packer, D. Plant, I. Simpson, P. Simpson, I. Sinclair, T. C. Somervaille, H. Small, G. J. Spencer, G. Thomson, M. Tonge, I. Waddell, J. Walsh, B. Waszkowycz, M. Wigglesworth, D. H. Wiseman, D. Ogilvie
Discovery And Optimization Of Allosteric Inhibitors Of Mutant Isocitrate Dehydrogenase 1 (R132H Idh1) Displaying Activity In Human Acute Myeloid Leukemia Cells.
J. Med. Chem. V. 59 11120 2016
PubMed-ID: 28002956

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
    Chains: A
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: JM109 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IDH1, PICD
    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

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
16N31Ligand/Ion(1~{R},5~{S})-3-[6-(3-METHYLBUTOXY)-5-[[(1~{R},3~{S})-5-OXIDANYL-2-ADAMANTYL]CARBAMOYL]PYRIDIN-2-YL]-3-AZABICYCLO[3.1.0]HEXANE-6-CARBOXYLIC ACID
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
16N32Ligand/Ion(1~{R},5~{S})-3-[6-(3-METHYLBUTOXY)-5-[[(1~{R},3~{S})-5-OXIDANYL-2-ADAMANTYL]CARBAMOYL]PYRIDIN-2-YL]-3-AZABICYCLO[3.1.0]HEXANE-6-CARBOXYLIC ACID
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:75 , ILE A:76 , THR A:77 , ARG A:82 , ASN A:96 , ASP A:279 , SER A:280 , 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 , ASN A:328 , HOH A:611binding site for residue NDP A 501
2AC2SOFTWAREARG A:119 , TRP A:124 , ILE A:130 , ASP A:252 , MET A:259 , TYR A:285 , HOH A:602binding site for residue 6N3 A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L57)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:137 -Gln A:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L57)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L57)

(-) Exons   (0, 0)

(no "Exon" information available for 5L57)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:409
                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.hhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhh.......hhhhhhhhhhh.eeeeee................eeeee...........eee...........................eee.....hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh....eeeee.................hhh.eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l57 A   3 KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDAARVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRLVSGWVKPIIIGHHAYGDQYRATDFVVPGPGKVEITYTPSDGTTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFAAAAIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL 414
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162|      175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405         
                                                                                                                                                                                         162|                                                                                                                                                                                                                                                        
                                                                                                                                                                                          166
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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 5L57)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L57)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L57)

(-) Gene Ontology  (30, 30)

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    Asp A:137 - Gln A:138   [ RasMol ]  
 
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  5l57
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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 5l58 5lge 5sun 5svf 5tqh

(-) Related Entries Specified in the PDB File

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