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(-) 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 :  1.58
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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, B
    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

  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
18HN2Ligand/Ion2-[(2~{S})-1-[3-CYANO-7-[(2-OXIDANYLIDENE-3,4-DIHYDRO-1~{H}-QUINOLIN-6-YL)AMINO]PYRAZOLO[1,5-A]PYRIMIDIN-5-YL]PYRROLIDIN-2-YL]ETHANOIC ACID
2CL2Ligand/IonCHLORIDE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
18HN1Ligand/Ion2-[(2~{S})-1-[3-CYANO-7-[(2-OXIDANYLIDENE-3,4-DIHYDRO-1~{H}-QUINOLIN-6-YL)AMINO]PYRAZOLO[1,5-A]PYRIMIDIN-5-YL]PYRROLIDIN-2-YL]ETHANOIC ACID
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18HN1Ligand/Ion2-[(2~{S})-1-[3-CYANO-7-[(2-OXIDANYLIDENE-3,4-DIHYDRO-1~{H}-QUINOLIN-6-YL)AMINO]PYRAZOLO[1,5-A]PYRIMIDIN-5-YL]PYRROLIDIN-2-YL]ETHANOIC ACID
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:114 , HIS A:116 , VAL A:117 , HOH A:319binding site for residue CL A 201
2AC2SOFTWAREMET A:51 , ALA A:52 , CYS A:53 , GLY A:55 , TYR A:58 , GLU A:81 , ASN A:84 , ASN A:96 , ARG A:98 , GLN A:113 , MET A:114 , GLU A:115 , HOH A:312 , HOH A:330 , HOH A:343 , HOH A:357 , HOH A:377 , ASN B:21 , ARG B:24 , LEU B:25 , ARG B:28binding site for residue 8HN A 202
3AC3SOFTWAREMET B:114 , HIS B:116 , VAL B:117 , HOH B:323binding site for residue CL B 201
4AC4SOFTWAREASN A:21 , ARG A:24 , LEU A:25 , ARG A:28 , MET B:51 , ALA B:52 , CYS B:53 , GLY B:55 , TYR B:58 , GLU B:81 , ASN B:84 , ASN B:96 , ARG B:98 , GLN B:113 , GLU B:115 , HOH B:315 , HOH B:316 , HOH B:338 , HOH B:345 , HOH B:365binding site for residue 8HN B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5N21)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5N21)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5N21)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5N21)

(-) Exons   (0, 0)

(no "Exon" information available for 5N21)

(-) 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    
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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:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhh........eee.....hhhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n21 A   7 SQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKAS 128
                                    16        26        36        46        56        66        76        86        96       106       116       126  


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhh........eee.....hhhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n21 B   7 SQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKAS 128
                                    16        26        36        46        56        66        76        86        96       106       116       126
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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 5N21)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5N21)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5N21)

(-) Gene Ontology  (59, 59)

Asymmetric Unit(hide GO term definitions)

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  5n21
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  BCL6_HUMAN | P41182
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 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 5n1x 5n1z 5n20 5x4m 5x4n 5x4o 5x4p 5x4q

(-) Related Entries Specified in the PDB File

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