Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) 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 :  2.60
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, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2SZ61Ligand/IonN-[4-(2-CHLORO-5-METHYLPYRIMIDIN-4-YL)PHENYL]-N-(4-{[(DIFLUOROACETYL)AMINO]METHYL}BENZYL)-2,4-DIHYDROXYBENZAMIDE
3TF31Ligand/IonN-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SZ62Ligand/IonN-[4-(2-CHLORO-5-METHYLPYRIMIDIN-4-YL)PHENYL]-N-(4-{[(DIFLUOROACETYL)AMINO]METHYL}BENZYL)-2,4-DIHYDROXYBENZAMIDE
3TF32Ligand/IonN-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:63 , PRO A:64 , VAL A:67 , MET A:122 , GLY A:125 , VAL A:126 , TYR A:129 , ASN A:142 , ILE A:143 , LEU A:147BINDING SITE FOR RESIDUE TF3 A 1367
2AC2SOFTWARELEU A:338BINDING SITE FOR RESIDUE MG A 1368
3AC3SOFTWARELYS 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:2029 , HOH A:2039BINDING SITE FOR RESIDUE SZ6 A 1369

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4V25)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4V25)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V25)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V25)

(-) Exons   (0, 0)

(no "Exon" information available for 4V25)

(-) 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    
   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:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...eeeeeee......hhhhhhhhhh..............hhhhhhhhhhh...eeeeeee...eeeeeeeee.hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v25 A   6 GSAPKYIEHFSKFSPSPLSMKQFLDFGSACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVY 366
                                    15        25       |37        47        57        67        77        87        97       107       117       127       137       147       157       167 ||    184       194       204       214       224       234       244       254       264       274       284       294       304|      323       333       343       353       363   
                                                      33|                                                                                                                                  169|                                                                                                                            304|                                                    
                                                       36                                                                                                                                   177                                                                                                                             314
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 4V25)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V25)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V25)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SZ6  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TF3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4v25)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4v25
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PDK2_HUMAN | Q15119
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PDK2_HUMAN | Q15119
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4v26 5j6a 5j71 5m4k 5m4m 5m4n 5m4p

(-) Related Entries Specified in the PDB File

4v26 VER-246608, A NOVEL PAN-ISOFORM ATP COMPETITIVE INHIBITOR OF PYRUVATE DEHYDROGENASE KINASE, DISRUPTS WARBURG METABOLISM AND INDUCES CONTEXT-DEPENDENT CYTOSTASIS IN CANCER CELLS