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
(-)Biological Unit 3
(-)Biological Unit 4
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE BCL6 BTB DOMAIN IN COMPLEX WITH PYRAZOLO-PYRIMIDINE LIGAND
 
Authors :  G. Robb, A. Ferguson, D. Hargreaves
Date :  06 Feb 17  (Deposition) - 17 May 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Mccoull, R. D. Abrams, E. Anderson, K. Blades, P. Barton, M. Box, J. Burgess, K. Byth, Q. Cao, C. Chuaqui, R. J. Carbajo, T. Cheung, E. Code, A. D. Ferguson, S. Fillery, N. O. Fuller, E. Gangl, N. Gao, M. Grist, D. Hargreaves, M. R. Howard, J. Hu, P. D. Kemmitt, J. E. Nelson N. O'Connell, D. B. Prince, P. Raubo, P. B. Rawlins, G. R. Robb, J. Shi, M. J. Waring, D. Whittaker, M. Wylot, X. Zhu
Discovery Of Pyrazolo[1, 5-A]Pyrimidine B-Cell Lymphoma 6 (Bcl6) Binders And Optimization To High Affinity Macrocycli Inhibitors.
J. Med. Chem. V. 60 4386 2017
PubMed-ID: 28485934  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00359

(-) Compounds

Molecule 1 - B-CELL LYMPHOMA 6 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Taxid: 4922
    Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BCL-6,B-CELL LYMPHOMA 5 PROTEIN,BCL-5,PROTEIN LAZ-3,ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 27,ZINC FINGER PROTEIN 51
 
Molecule 2 - B-CELL LYMPHOMA 6 PROTEIN
    Chains: B, C
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Taxid: 4922
    Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BCL-6,B-CELL LYMPHOMA 5 PROTEIN,BCL-5,PROTEIN LAZ-3,ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 27,ZINC FINGER PROTEIN 51
 
Molecule 3 - B-CELL LYMPHOMA 6 PROTEIN
    Chains: D
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Taxid: 4922
    Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BCL-6,B-CELL LYMPHOMA 5 PROTEIN,BCL-5,PROTEIN LAZ-3,ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 27,ZINC FINGER PROTEIN 51

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
18HH4Ligand/Ion~{N}-ETHYL-5-PYRIDIN-3-YL-PYRAZOLO[1,5-A]PYRIMIDIN-7-AMINE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
18HH-1Ligand/Ion~{N}-ETHYL-5-PYRIDIN-3-YL-PYRAZOLO[1,5-A]PYRIMIDIN-7-AMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
18HH2Ligand/Ion~{N}-ETHYL-5-PYRIDIN-3-YL-PYRAZOLO[1,5-A]PYRIMIDIN-7-AMINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
18HH1Ligand/Ion~{N}-ETHYL-5-PYRIDIN-3-YL-PYRAZOLO[1,5-A]PYRIMIDIN-7-AMINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
18HH1Ligand/Ion~{N}-ETHYL-5-PYRIDIN-3-YL-PYRAZOLO[1,5-A]PYRIMIDIN-7-AMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:51 , ALA A:52 , TYR A:58 , ASN B:21 , ARG B:24 , LEU B:25 , GLU D:81 , ASN D:84binding site for residue 8HH B 201
2AC2SOFTWAREASN A:21 , ARG A:24 , LEU A:25 , MET B:51 , TYR B:58binding site for residue 8HH B 202
3AC3SOFTWAREASN C:21 , ARG C:24 , LEU C:25 , MET D:51 , ALA D:52 , TYR D:58binding site for residue 8HH C 201
4AC4SOFTWAREGLU B:81 , ASN B:84 , ILE B:85 , MET C:51 , SER C:54 , GLY C:55 , TYR C:58 , ASN D:21 , ARG D:24 , LEU D:25binding site for residue 8HH D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5N1X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5N1X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5N1X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5N1X)

(-) Exons   (0, 0)

(no "Exon" information available for 5N1X)

(-) 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:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhh.......eee.....hhhhhhhhhhhhhhheee....hhhhhhhhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n1x A   8 QIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTARKFIKAS 128
                                    17        27        37        47        57        67        77        87        97       107       117       127 


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n1x B   7 SQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTARKFIKA 127
                                    16        26        36        46        56        66        76        86        96       106       116       126 


Chain C from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhee.....hhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n1x C   7 SQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTARKFIKA 127
                                    16        26        36        46        56        66        76        86        96       106       116       126 


Chain D from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhheee....hhhhhhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5n1x D   8 QIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTARKFI 125
                                    17        27        37        47        57        67        77        87        97       107       117
   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 5N1X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5N1X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5N1X)

(-) Gene Ontology  (59, 59)

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
    8HH  [ 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 5n1x)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 3 PNG format | Biol. Unit 4 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
  5n1x
    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
  BCL6_HUMAN | P41182
    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)
  (no 'Enzyme Classificator' available)
    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
  BCL6_HUMAN | P41182
    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
        BCL6_HUMAN | P41182: 1r28 1r29 1r2b 2en2 2eos 2lce 2yrm 3bim 3e4u 3lbz 4cp3 4u2m 5h7g 5h7h 5n1z 5n20 5n21 5x4m 5x4n 5x4o 5x4p 5x4q

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5N1X)