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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 2 IN COMPLEX WITH INHIBITOR PS46
 
Authors :  W. J. Gui, S. C. Tso, J. L. Chuang, C. Y. Wu, X. Qi, R. M. Wynn, D. T. Chuang
Date :  04 Apr 16  (Deposition) - 25 Jan 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
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
(for further references see the PDB file header)

(-) 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1P461Ligand/Ion(3S)-3-AMINO-4-[4-({2-[(2,4-DIHYDROXYPHENYL)SULFONYL]-2H-ISOINDOL-5-YL}AMINO)PIPERIDIN-1-YL]-4-OXOBUTANAMIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1P462Ligand/Ion(3S)-3-AMINO-4-[4-({2-[(2,4-DIHYDROXYPHENYL)SULFONYL]-2H-ISOINDOL-5-YL}AMINO)PIPERIDIN-1-YL]-4-OXOBUTANAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:252 , ASN A:255 , ALA A:259 , GLU A:262 , SER A:263 , GLU A:265 , ASP A:290 , GLY A:294 , VAL A:295 , THR A:354 , HOH A:603 , HOH A:609 , HOH A:630 , HOH A:639 , HOH A:655binding site for residue P46 A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J6A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5J6A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...eeeeeeee.....hhhhhhhhh..........hhhhhhhhhhhh..eeeeeee...eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j6a A  11 ASLAGAPKYIEHFSKFSPSPLSMKQFLDFGSCEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPV 373
                                    20        30        40||      53        63        73        83        93       103       113       123       133       143       153       163       173   ||  192       202       212       222       232       242       252       262       272       282       292       302       326       336       346       356       366       
                                                         41|                                                                                                                                 177|                                                                                                                        310|                                                
                                                          45                                                                                                                                  187                                                                                                                         325
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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 5J6A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J6A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J6A)

(-) Gene Ontology  (26, 26)

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 Related Entries

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UniProtKB/Swiss-Prot
        PDK2_HUMAN | Q15119: 2btz 2bu2 2bu5 2bu6 2bu7 2bu8 4mp2 4mp7 4mpc 4mpe 4mpn 4v25 4v26 5j71 5m4k 5m4m 5m4n 5m4p

(-) Related Entries Specified in the PDB File

4mp2 4MP2 CONTAINS THESAME PROTEIN WITH DIFFERENT COMPOUND.
4mp7 4MP7 CONTAINS THESAME PROTEIN WITH DIFFERENT COMPOUND.
4mpc 4MPC CONTAINS THESAME PROTEIN WITH DIFFERENT COMPOUND.
4mpe 4MPE CONTAINS THESAME PROTEIN WITH DIFFERENT COMPOUND.
4mpn 4MPN CONTAINS THESAME PROTEIN WITH DIFFERENT COMPOUND.
5j71 5J71 CONTAINS THE SAME PROTEIN WITH DIFFERENT COMPOUND.