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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TNKS2 IN COMPLEX WITH 2-(2,4-DICHLOROPHENYL)-1-METHYL-1H,2H,3H,4H-PYRIDO(2,3-D) PYRIMIDIN-4-ONE
 
Authors :  Y. Nkizinkiko, L. Lehtio
Date :  06 Mar 15  (Deposition) - 29 Jul 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Protein-Ligand Complex, Diphtheria Toxin Like Fold, Adp- Ribosylation, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Nkizinkiko, B. V. S. Suneel Kumar, V. U. Jeankumar, T. Haikarainen J. Koivunen, C. Madhuri, P. Yogeeswari, H. Venkannagari, E. Obaji, T. Pihlajaniemi, D. Sriram, L. Lehtio
Discovery Of Potent And Selective Nonplanar Tankyrase Inhibiting Nicotinamide Mimics.
Bioorg. Med. Chem. V. 23 4139 2015
PubMed-ID: 26183543  |  Reference-DOI: 10.1016/J.BMC.2015.06.063

(-) Compounds

Molecule 1 - TANKYRASE 2
    Chains: A, B
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2
    Fragment: CATALYTIC DOMAIN, RESIDUES 946-1162
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TANK2, ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6, POLY ADP-RIBOSE POLYMERASE 5B, TNKS-2, TRF1-INTERACTING ANKYRIN -RELATED ADP-RIBOSE POLYMERASE 2, TANKYRASE II, TANKYRASE-LIKE PROTEIN, TANKYRASE-RELATED PROTEIN, ARTD6

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
3TGW2Ligand/Ion(2R)-2-(2,4-DICHLOROPHENYL)-1-METHYL-2,3-DIHYDROPYRIDO[2,3-D]PYRIMIDIN-4-ONE
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
3TGW1Ligand/Ion(2R)-2-(2,4-DICHLOROPHENYL)-1-METHYL-2,3-DIHYDROPYRIDO[2,3-D]PYRIMIDIN-4-ONE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
3TGW1Ligand/Ion(2R)-2-(2,4-DICHLOROPHENYL)-1-METHYL-2,3-DIHYDROPYRIDO[2,3-D]PYRIMIDIN-4-ONE
4ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:1081 , HIS A:1084 , CYS A:1089 , CYS A:1092BINDING SITE FOR RESIDUE ZN A3162
02AC2SOFTWARECYS B:1081 , HIS B:1084 , CYS B:1089 , CYS B:1092BINDING SITE FOR RESIDUE ZN B3162
03AC3SOFTWAREARG A:977 , HIS A:979 , ARG A:980 , LYS A:1067 , GLN A:1070 , HOH A:2121 , HOH A:2123 , HOH A:2168BINDING SITE FOR RESIDUE SO4 A3163
04AC4SOFTWAREARG B:977 , HIS B:979 , ARG B:980 , LYS B:1067 , GLN B:1070 , HOH B:2030 , HOH B:2032 , HOH B:2105BINDING SITE FOR RESIDUE SO4 B3163
05AC5SOFTWAREASN A:990 , ARG A:991 , PRO A:1160 , GLU A:1161 , HOH A:2053 , HOH A:2055BINDING SITE FOR RESIDUE SO4 A3164
06AC6SOFTWAREASN B:990 , ARG B:991 , PRO B:1160 , GLU B:1161 , HOH B:2043 , HOH B:2046 , HOH B:2157BINDING SITE FOR RESIDUE SO4 B3164
07AC7SOFTWAREARG B:977 , HIS B:979 , GLY B:983 , GLY B:987 , ILE B:988 , PHE B:989 , HOH B:2042BINDING SITE FOR RESIDUE GOL B3165
08AC8SOFTWARESER A:974 , THR A:975 , VAL A:976 , ASN A:1064 , PHE A:1110 , LEU A:1134 , LEU A:1136BINDING SITE FOR RESIDUE GOL A3165
09AC9SOFTWAREARG A:1128 , PRO A:1129 , SER A:1130 , VAL A:1131 , ASN A:1132 , GLY A:1133BINDING SITE FOR RESIDUE GOL A3166
10BC1SOFTWAREARG A:977 , HIS A:979 , GLY A:983 , GLY A:987 , ILE A:988 , PHE A:989 , HOH A:2052BINDING SITE FOR RESIDUE GOL A3167
11BC2SOFTWAREHIS A:1031 , GLY A:1032 , PHE A:1035 , HIS A:1048 , TYR A:1050 , GLY A:1058 , TYR A:1060 , PHE A:1061 , SER A:1068 , TYR A:1071 , GLU A:1138 , HOH A:2128BINDING SITE FOR RESIDUE TGW A3168
12BC3SOFTWAREHIS B:1031 , GLY B:1032 , PHE B:1035 , HIS B:1048 , TYR B:1050 , TYR B:1060 , PHE B:1061 , ALA B:1062 , SER B:1068 , TYR B:1071 , GLU B:1138 , HOH B:2109BINDING SITE FOR RESIDUE TGW B3166

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AL3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AL3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AL3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AL3)

(-) Exons   (0, 0)

(no "Exon" information available for 5AL3)

(-) 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:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh................eeeeeeeeeehhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhh.hhhhh.........eeee.hhhhhhh...hhhhh...............eeeeeeeee...eeeeee..........eeeeee........eeee.hhh.eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5al3 A  952 GTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPE 1161
                                   961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111||    1123      1133      1143      1153        
                                                                                                                                                                                         1112|                                              
                                                                                                                                                                                          1115                                              


Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh................eeeeeeeeeehhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhh.hhhhh.........eeee.hhhhhhh...hhhhh...............eeeeeeeee...eeeeee............eeeeee........eeee.hhh.eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5al3 B  952 GTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPE 1161
                                   961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161
   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 5AL3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AL3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AL3)

(-) Gene Ontology  (29, 29)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TGW  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5al3)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  5al3
    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
  TNKS2_HUMAN | Q9H2K2
    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)
  2.4.2.30
    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
  TNKS2_HUMAN | Q9H2K2
    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
        TNKS2_HUMAN | Q9H2K2: 2y0i 3kr7 3kr8 3mhj 3mhk 3p0n 3p0p 3p0q 3twq 3twr 3tws 3twt 3twu 3twv 3tww 3twx 3u9h 3u9y 3ua9 3w51 4avu 4avw 4bfp 4bj9 4bjb 4bjc 4bs4 4bu3 4bu5 4bu6 4bu7 4bu8 4bu9 4bua 4bud 4bue 4buf 4bui 4bus 4but 4buu 4buv 4buw 4bux 4buy 4hki 4hkk 4hkn 4hl5 4hlf 4hlg 4hlh 4hlk 4hlm 4hmh 4hyf 4iue 4j1z 4j21 4j22 4j3l 4j3m 4kzl 4kzq 4kzu 4l09 4l0b 4l0i 4l0s 4l0t 4l0v 4l10 4l2f 4l2g 4l2k 4l31 4l32 4l33 4l34 4m7b 4pml 4pnl 4pnm 4pnn 4pnq 4pnr 4pns 4pnt 4tju 4tjw 4tjy 4tk0 4tk5 4tkf 4tkg 4tki 4ufu 4ufy 4uhg 4ui3 4ui4 4ui5 4ui6 4ui7 4ui8 4uvl 4uvn 4uvo 4uvp 4uvs 4uvt 4uvu 4uvv 4uvw 4uvx 4uvy 4uvz 4ux4 4w5i 4z68 5adq 5adr 5ads 5adt 5aeh 5aku 5akw 5al1 5al2 5al4 5al5 5bxo 5bxu 5c5p 5c5q 5c5r 5dcz 5fpf 5fpg 5jrt

(-) Related Entries Specified in the PDB File

5aku CRYSTAL STRUCTURE OF TNKS2 IN COMPLEX WITH 2-(4-TERT -BUTYLPHENYL)-1,2,3,4-TETRAHYDROQUINAZOLIN-4-ONE
5akw CRYSTAL STRUCTURE OF TNKS2 IN COMPLEX WITH 2-(4- CHLOROPHENYL)-1,2,3,4-TETRAHYDROQUINAZOLIN-4-ONE
5al1 CRYSTAL STRUCTURE OF TNKS2 IN COMPLEX WITH 2-(4-TERT -BUTYLPHENYL)-1H,2H,3H,4H-PYRIDO(2,3-D)PYRIMIDIN- 4-ONE
5al2 CRYSTAL STRUCTURE OF TNKS2 IN COMPLEX WITH 2-(4-( PROPAN-2-YL)PHENYL)-1H,2H,3H,4H-PYRIDO(2,3-D) PYRIMIDIN-4-ONE
5al4 CRYSTAL STRUCTURE OF TNKS2 IN COMPLEX WITH 2-(4- METHYLPIPERAZIN-1-YL)-3,4,5,6,7,8- HEXAHYDROQUINAZOLIN-4-ONE