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(-) Description

Title :  VER-246608, A NOVEL PAN-ISOFORM ATP COMPETITIVE INHIBITOR OF PYRUVATE DEHYDROGENASE KINASE, DISRUPTS WARBURG METABOLISM AND INDUCES CONTEXT- DEPENDENT CYTOSTASIS IN CANCER CELLS
 
Authors :  J. D. Moore, A. Staniszewska, T. Shaw, J. D'Alessandro, B. Davis, A. Sur L. Baker, N. Matassova, J. Murray, A. Macias, P. Brough, M. Wood, P. C. M
Date :  06 Oct 14  (Deposition) - 03 Dec 14  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Glycolysis, Warburg Metabolism, Nov3R (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Moore, A. Staniszewska, T. Shaw, J. D'Alessandro, B. Davis, A. Surgenor, L. Baker, N. Matassova, J. Murray, A. Macias, P. Brough, M. Wood, P. C. Mahon
Ver-246608, A Novel Pan-Isoform Atp Competitive Inhibitor O Pyruvate Dehydrogenase Kinase, Disrupts Warburg Metabolism And Induces Context-Dependent Cytostasis In Cancer Cells.
Oncotarget V. 5 12862 2014
PubMed-ID: 25404640

(-) 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 Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: KINASE DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PYRUVATE DEHYDROGENASE KINASE ISOFORM 2, PDH KINASE 2, PDKI I

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
17TJ1Ligand/IonN-[4-(2-CHLORO-5-METHYLPYRIMIDIN-4-YL)PHENYL]-2,4-DIHYDROXY-N-(4-{[(TRIFLUOROACETYL)AMINO]METHYL}BENZYL)BENZAMIDE
2MG2Ligand/IonMAGNESIUM ION
3TF31Ligand/IonN-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
17TJ2Ligand/IonN-[4-(2-CHLORO-5-METHYLPYRIMIDIN-4-YL)PHENYL]-2,4-DIHYDROXY-N-(4-{[(TRIFLUOROACETYL)AMINO]METHYL}BENZYL)BENZAMIDE
2MG-1Ligand/IonMAGNESIUM ION
3TF32Ligand/IonN-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:64 , ARG A:66 , VAL A:67 , VAL A:126 , TYR A:129 , ASN A:142 , ILE A:143BINDING SITE FOR RESIDUE TF3 A 1367
2AC2SOFTWARELEU A:338BINDING SITE FOR RESIDUE MG A 1368
3AC3SOFTWARESER A:41BINDING SITE FOR RESIDUE MG A 1369
4AC4SOFTWARELYS A:246 , ASN A:247 , ARG A:250 , ALA A:251 , GLU A:254 , ASP A:282 , GLY A:284 , GLY A:286 , VAL A:287 , THR A:346 , HOH A:2067 , HOH A:2084BINDING SITE FOR RESIDUE 7TJ A 1370

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4V26)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4V26)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V26)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V26)

(-) Exons   (0, 0)

(no "Exon" information available for 4V26)

(-) Sequences/Alignments

Asymmetric Unit
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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:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhhhhhhhhhhh.....eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee...eeeeeee......hhhhhhhhhh.......hhhhh..hhhhhhhhhhh...eeeeeee...eeeeeeeee.hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v26 A   6 ASAPKYIEHFSKFSPSPLSMKQFLDFGSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVY 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 4V26)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V26)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V26)

(-) Gene Ontology  (26, 26)

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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 5j6a 5j71 5m4k 5m4m 5m4n 5m4p

(-) Related Entries Specified in the PDB File

4v25 VER-246608, A NOVEL PAN-ISOFORM ATP COMPETITIVE INHIBITOR OF PYRUVATE DEHYDROGENASE KINASE, DISRUPTS WARBURG METABOLISM AND INDUCES CONTEXT-DEPENDENT CYTOSTASIS IN CANCER CELLS