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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 2 IN COMPLEX WITH INHIBITOR PS35
 
Authors :  W. J. Gui, S. C. Tso, J. L. Chuang, C. Y. Wu, X. Qi, R. M. Wynn, D. T. Chuang
Date :  05 Apr 16  (Deposition) - 25 Jan 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ghkl Protein Kinase, Pyruvate Dehydrogenase Complex, Mitochondrial Protein Kinases, Impaired Glucose Oxidation, Hepatic Steatosis, Type 2 Diabetes, Cancer, Bergerat Nucleotide-Binding Fold, Protein Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Tso, M. Lou, C. Y. Wu, W. J. Gui, J. L. Chuang, L. K. Morlock, N. S. Williams, R. M. Wynn, X. Qi, D. T. Chuang
Development Of Dihydroxyphenyl Sulfonylisoindoline Derivatives As Liver-Targeting Pyruvate Dehydrogenase Kinas Inhibitors.
J. Med. Chem. V. 60 1142 2017
PubMed-ID: 28085286  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01540

(-) Compounds

Molecule 1 - [PYRUVATE DEHYDROGENASE (ACETYL-TRANSFERRING)] KINASE ISOZYME 2, MITOCHONDRIAL
    Chains: A
    EC Number: 2.7.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PDK2, PDHK2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PYRUVATE DEHYDROGENASE KINASE ISOFORM 2,PDKII

 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
1P351Ligand/Ion4-({5-[(PIPERIDIN-4-YL)AMINO]-1,3-DIHYDRO-2H-ISOINDOL-2-YL}SULFONYL)BENZENE-1,3-DIOL
2TLA1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1P352Ligand/Ion4-({5-[(PIPERIDIN-4-YL)AMINO]-1,3-DIHYDRO-2H-ISOINDOL-2-YL}SULFONYL)BENZENE-1,3-DIOL
2TLA2Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:262 , SER A:263 , HIS A:264 , GLU A:265 , SER A:266 , P35 A:502 , HOH A:608 , HOH A:622 , HOH A:702 , HOH A:737binding site for residue TLA A 501
2AC2SOFTWARELEU A:252 , ASN A:255 , ALA A:259 , GLU A:262 , ASP A:290 , GLY A:294 , VAL A:295 , THR A:354 , TLA A:501 , HOH A:623 , HOH A:644 , HOH A:674 , HOH A:681 , HOH A:702binding site for residue P35 A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J71)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5J71)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J71)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J71)

(-) Exons   (0, 0)

(no "Exon" information available for 5J71)

(-) 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    
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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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh......hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee.......eeeehhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee...eeeeeeee.....hhhhhhhhhh...hhhhhhhhhhhhh..eeeeeee...eeeeeeeee.............hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j71 A  12 SLAGAPKYIEHFSKFSPSPLSMKQFLDCEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVYNKSAWRHYDWC 392
                                    21        31      ||47        57        67        77        87        97       107       117       127       137       147       157       167       187       197       207       217       227    || 238       248       258       268       278       288       298       327       337       347       357       367       377    ||  
                                                     38|                                                                                                                                176|                                          232|                                                                      307|                                                    382|  
                                                      45                                                                                                                                 187                                           234                                                                       327                                                     390
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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 5J71)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J71)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J71)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PDK2_HUMAN | Q15119: 2btz 2bu2 2bu5 2bu6 2bu7 2bu8 4mp2 4mp7 4mpc 4mpe 4mpn 4v25 4v26 5j6a 5m4k 5m4m 5m4n 5m4p

(-) Related Entries Specified in the PDB File

4mp2 4MP2 CONTAINS THE SAME PROTEIN WITH DIFFERENT COMPOUND.
4mp7 4MP7 CONTAINS THE SAME PROTEIN WITH DIFFERENT COMPOUND.
4mpc 4MPC CONTAINS THE SAME PROTEIN WITH DIFFERENT COMPOUND.
4mpe 4MPE CONTAINS THE SAME PROTEIN WITH DIFFERENT COMPOUND.
4mpn 4MPN CONTAINS THE SAME PROTEIN WITH DIFFERENT COMPOUND.
5j6a 5J6A CONTAINS THE SAME PROTEIN WITH DIFFERENT COMPOUND.