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 :  CO-CRYSTAL STRUCTURE OF TNKS1 WITH COMPOUND 18 [4-[(4S)-5,5-DIMETHYL-2-OXO-4-PHENYL-1,3-OXAZOLIDIN-3-YL]-N-(QUINOLIN-8-YL)BENZAMIDE]
 
Authors :  X. Huang, H. Bregman, C. Wilson, E. Dimauro, H. Gunaydin
Date :  12 Apr 13  (Deposition) - 05 Jun 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Parp, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Bregman, N. Chakka, A. Guzman-Perez, H. Gunaydin, Y. Gu, X. Huang, V. Berry, J. Liu, Y. Teffera, L. Huang, B. Egge, E. L. Mullady, S. Schneider, P. S. Andrews, A. Mishra, J. Newcomb, R. Serafino, C. A. Strathdee, S. M. Turci, C. Wilson, E. F. Dimauro
Discovery Of Novel, Induced-Pocket Binding Oxazolidinones A Potent, Selective, And Orally Bioavailable Tankyrase Inhibitors.
J. Med. Chem. V. 56 4320 2013
PubMed-ID: 23701517  |  Reference-DOI: 10.1021/JM4000038

(-) Compounds

Molecule 1 - TANKYRASE-1
    Chains: A, B
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PARP CATALYTIC, UNP RESIDUES 1104-1314
    Gene: TNKS, PARP5A, PARPL, TIN1, TINF1, TNKS1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TANK1, ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 5, ARTD5, POLY [ADP-RIBOSE] POLYMERASE 5A, TNKS-1, TRF1-INTERACTING ANKYRIN-RELATED ADP-RIBOSE POLYMERASE, TANKYRASE I

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1K4F2Ligand/Ion4-[(4S)-5,5-DIMETHYL-2-OXO-4-PHENYL-1,3-OXAZOLIDIN-3-YL]-N-(QUINOLIN-8-YL)BENZAMIDE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1K4F1Ligand/Ion4-[(4S)-5,5-DIMETHYL-2-OXO-4-PHENYL-1,3-OXAZOLIDIN-3-YL]-N-(QUINOLIN-8-YL)BENZAMIDE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1K4F1Ligand/Ion4-[(4S)-5,5-DIMETHYL-2-OXO-4-PHENYL-1,3-OXAZOLIDIN-3-YL]-N-(QUINOLIN-8-YL)BENZAMIDE
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1234 , HIS A:1237 , CYS A:1242 , CYS A:1245BINDING SITE FOR RESIDUE ZN A 1401
2AC2SOFTWAREHIS A:1184 , PRO A:1187 , PHE A:1188 , ALA A:1191 , ILE A:1192 , GLY A:1196 , ASP A:1198 , HIS A:1201 , GLY A:1209 , GLY A:1211 , ILE A:1212 , TYR A:1213BINDING SITE FOR RESIDUE K4F A 1402
3AC3SOFTWARECYS B:1234 , HIS B:1237 , CYS B:1242 , CYS B:1245BINDING SITE FOR RESIDUE ZN B 1401
4AC4SOFTWAREHIS B:1184 , PRO B:1187 , PHE B:1188 , ALA B:1191 , GLY B:1196 , PHE B:1197 , ASP B:1198 , HIS B:1201 , TYR B:1203 , GLY B:1206 , GLY B:1211 , ILE B:1212 , TYR B:1213 , GLY B:1227BINDING SITE FOR RESIDUE K4F B 1402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K4F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K4F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K4F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K4F)

(-) Exons   (0, 0)

(no "Exon" information available for 4K4F)

(-) 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:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh................eeeeeeeeeehhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhh.hhhhh.........eee..hhhhhhhh..hhhhh...............eeeeeeeee...eeee..............eeee........eeee.hhh.eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4k4f A 1104 QGTILLDLAPEDKEYQSVEEEMQSTIREHRDGGNAGGIFNRYNVIRIQKVVNKKLRERFCHRQKEVSEENHNHHNERMLFHGSPFINAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPTHKDRSCYICHRQMLFCRVTLGKSFLQFSTMKMAHAPPGHHSVIGRPSVLAYAEYVIYRGEQAYPEYLITYQIMKPEH 1315
                                  1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283||    1295      1305      1315
                                                                                                                                                                                                             1284|                            
                                                                                                                                                                                                              1287                            


Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh................eeeeeeeeeehhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhh.hhhhh.......eeee.hhhhhhhhh.....................eeeeeeeee...eee...............eeee...eeee.hhh.eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4k4f B 1104 QGTILLDLAPEDKEYQSVEEEMQSTIREHRDGGNAGGIFNRYNVIRIQKVVNKKLRERFCHRQKEVSEENHNHHNERMLFHGSPFINAIIHKGFDERHAYGMFGAGIYFAENSSKSNQYVYGIGGGTGCPTHKDRSCYICHRQMLFCRVTLGKSFLQFSTMKMAHAPPGHHSVIGRYAEYVIYRGEQAYPEYLITYQIMKPEH 1315
                                  1113      1123      1133      1143      1153      1163      1173      1183      1193      1203|     1215      1225      1235      1245      1255      1265      1275     |1292      1302      1312   
                                                                                                                            1203|                                                                       1281|                          
                                                                                                                             1206                                                                        1289
   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 4K4F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K4F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K4F)

(-) Gene Ontology  (46, 46)

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
    K4F  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4k4f)
 
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
  4k4f
    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
  TNKS1_HUMAN | O95271
    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
  TNKS1_HUMAN | O95271
    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
        TNKS1_HUMAN | O95271: 2rf5 3udd 3uh2 3uh4 4dvi 4i9i 4k4e 4krs 4li6 4li7 4li8 4msg 4msk 4mt9 4n3r 4n4v 4oa7 4tor 4tos 4u6a 4uuh 4uw1 4w5s 4w6e 5ebt 5ece 5ety 5gp7 5jhq 5jti 5ju5 5kni

(-) Related Entries Specified in the PDB File

4dvi 4k4e