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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BROMODOMAIN OF BRD9 IN COMPLEX WITH COMPOUND 9.
 
Authors :  G. Bader, L. J. Martin, S. Steurer, A. Weiss-Puxbaum, A. Zoephel
Date :  30 Nov 15  (Deposition) - 09 Mar 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bromodomain, Inhibitor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Martin, M. Koegl, G. Bader, X. L. Cockcroft, O. Fedorov, D. Fiegen T. Gerstberger, M. H. Hofmann, A. F. Hohmann, D. Kessler, S. Knapp, P. Knesl, S. Kornigg, S. Muller, H. Nar, C. Rogers, K. Rumpel, O. Schaaf S. Steurer, C. Tallant, C. R. Vakoc, M. Zeeb, A. Zoephel, M. Pearson, G. Boehmelt, D. Mcconnell
Structure-Based Design Of An In Vivo Active Selective Brd9 Inhibitor.
J. Med. Chem. V. 59 4462 2016
PubMed-ID: 26914985  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01865

(-) Compounds

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 9
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: BROMODOMAIN, UNP RESIDUES 14-134
    Gene: BRD9
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
15U22Ligand/Ion5-[3,5-DIMETHOXY-4-[(3-OXIDANYLAZETIDIN-1-YL)METHYL]PHENYL]-1,3-DIMETHYL-PYRIDIN-2-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15U21Ligand/Ion5-[3,5-DIMETHOXY-4-[(3-OXIDANYLAZETIDIN-1-YL)METHYL]PHENYL]-1,3-DIMETHYL-PYRIDIN-2-ONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15U21Ligand/Ion5-[3,5-DIMETHOXY-4-[(3-OXIDANYLAZETIDIN-1-YL)METHYL]PHENYL]-1,3-DIMETHYL-PYRIDIN-2-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:42 , PHE A:44 , PHE A:45 , PHE A:47 , VAL A:49 , TYR A:99 , ASN A:100 , TYR A:106 , HOH A:301binding site for residue 5U2 A 201
2AC2SOFTWAREHIS A:115 , LYS A:119 , HIS B:42 , GLY B:43 , PHE B:44 , PHE B:45 , PHE B:47 , VAL B:49 , ALA B:54 , TYR B:99 , ASN B:100 , TYR B:106 , HOH B:301binding site for residue 5U2 B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F1L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F1L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F1L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F1L)

(-) Exons   (0, 0)

(no "Exon" information available for 5F1L)

(-) 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:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.................hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 5f1l A  22 STPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKERLLALKRSMS 134
                                    31        41        51        61        71        81        91       101       111       121       131   


Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh................hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5f1l B  21 ESTPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKERLLALKRSMS 134
                                    30        40        50        60        70        80        90       100       110       120       130
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  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 5F1L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F1L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F1L)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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  BRD9_HUMAN | Q9H8M2
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BRD9_HUMAN | Q9H8M2: 3hme 4nqn 4uit 4uiu 4uiv 4uiw 4xy8 4yy4 4yy6 4yyd 4yyg 4yyh 4yyi 4yyj 4yyk 4z6h 4z6i 5e9v 5eu1 5f1h 5f25 5f2p 5i40 5i7x 5i7y 5igm 5ign 5ji8

(-) Related Entries Specified in the PDB File

5eu1 5f1h