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(-) Description

Title :  APPLICATION OF OFF-RATE SCREENING IN THE IDENTIFICATION OF NOVEL PAN-ISOFORM INHIBITORS OF PYRUVATE DEHYDROGENASE KINASE
 
Authors :  L. M. Baker, P. Brough, A. Surgenor
Date :  18 Oct 16  (Deposition) - 22 Feb 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Off-Rate Screening, Pdhk, Hsp90, Spr, Kinase Inhibitors, Fragment Screening, Cancer, Pdk1, Pdk2, Pdk3, Pdk4, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Brough, L. Baker, S. Bedford, K. Brown, S. Chavda, V. Chell, J. D'Alessandro, N. G. Davies, B. Davis, L. Le Strat, A. T. Macias, D. Maddox, P. C. Mahon, A. J. Massey, N. Matassova, S. Mckenna, J. W. Meissner, J. D. Moore, J. B. Murray, C. J. Northfield, C. Parry, R. Parsons, S. D. Roughley, T. Shaw, H. Simmonite, S. Stokes, A. Surgenor, E. Stefaniak, A. Robertson, Y. Wang, P. Webb, N. Whitehead, M. Wood
Application Of Off-Rate Screening In The Identification Of Novel Pan-Isoform Inhibitors Of Pyruvate Dehydrogenase Kinase.
J. Med. Chem. V. 60 2271 2017
PubMed-ID: 28199108  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01478

(-) 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 BL21(DE3)
    Expression System Taxid: 469008
    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/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
17FW1Ligand/Ion~{N}-[4-[METHYL(QUINOXALIN-6-YLMETHYL)CARBAMOYL]PHENYL]-2,4-BIS(OXIDANYL)-~{N}-(PHENYLMETHYL)BENZAMIDE
2CL3Ligand/IonCHLORIDE ION
3TF31Ligand/IonN-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:244 , ASN A:247 , ARG A:250 , ALA A:251 , ASP A:282 , GLY A:284 , GLY A:286 , VAL A:287 , LEU A:295 , TYR A:300 , SER A:301 , ALA A:316 , GLY A:317 , PHE A:318 , GLY A:319 , LEU A:338 , THR A:346 , HOH A:506 , HOH A:511binding site for residue 7FW A 401
2AC2SOFTWARELEU A:63 , PRO A:64 , ARG A:66 , VAL A:67 , GLY A:125 , VAL A:126 , TYR A:129 , ASN A:142 , ILE A:143 , LEU A:147binding site for residue TF3 A 402
3AC3SOFTWAREHOH A:595binding site for residue CL A 403
4AC4SOFTWARELEU A:338binding site for residue CL A 404
5AC5SOFTWARESER A:41binding site for residue CL A 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M4M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5M4M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M4M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M4M)

(-) Exons   (0, 0)

(no "Exon" information available for 5M4M)

(-) 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:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...eeeeeee......hhhhhhhhhh.............hhhhhhhhhhhh...eeeeeee...eeeeeeeee.hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m4m A   6 GSAPKYIEHFSKFSPSPLSMKQFLDFGSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVY 366
                                    15        25       |36        46        56        66        76        86        96       106       116       126       136       146       156       166  ||   183       193       203       213       223       233       243       253       263       273       283       293       303||     322       332       342       352       362    
                                                      33|                                                                                                                                   169|                                                                                                                            304|                                                    
                                                       35                                                                                                                                    177                                                                                                                             314
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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 5M4M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M4M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M4M)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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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 5j71 5m4k 5m4n 5m4p

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5M4M)