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(-) Description

Title :  BROMODOMAIN OF HUMAN BRPF1 WITH N-1,3-DIMETHYL-6-2R-2-METHYLPIPERAZIN-1-YL-2-OXO-2,3-DIHYDRO-1H-1,3-BENZODIAZOL-5-YL-2-METHOXYBENZAMIDE
 
Authors :  C. Chung
Date :  16 May 16  (Deposition) - 06 Jul 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
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 :  Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Bamborough, H. A. Barnett, I. Becher, M. J. Bird, C. Chung, P. D. Craggs, E. H. Demont, H. Diallo, D. J. Fallon, L. J. Gordon, P. Grandi, C. I. Hobbs, E. Hooper-Greenhill, E. J. Jones, R. P. Law, A. Le Gall, D. Lugo, A. Michon, D. J. Mitchell, R. K. Prinjha, R. J. Sheppard, A. J. B. Watson, R. J. Watson
Gsk6853, A Chemical Probe For Inhibition Of The Brpf1 Bromodomain.
Acs Med. Chem. Lett. V. 7 552 2016
PubMed-ID: 27326325  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00092

(-) Compounds

Molecule 1 - PEREGRIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: BROMODOMAIN OF BRPF1, UNP RESIDUES 622-738
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1, PROTEIN BR140,

 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
1LF14Ligand/IonN-[1,3-DIMETHYL-6-[(2R)-2-METHYLPIPERAZIN-1-YL]-2-OXIDANYLIDENE-BENZIMIDAZOL-5-YL]-2-METHOXY-BENZAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1LF11Ligand/IonN-[1,3-DIMETHYL-6-[(2R)-2-METHYLPIPERAZIN-1-YL]-2-OXIDANYLIDENE-BENZIMIDAZOL-5-YL]-2-METHOXY-BENZAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1LF11Ligand/IonN-[1,3-DIMETHYL-6-[(2R)-2-METHYLPIPERAZIN-1-YL]-2-OXIDANYLIDENE-BENZIMIDAZOL-5-YL]-2-METHOXY-BENZAMIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1LF11Ligand/IonN-[1,3-DIMETHYL-6-[(2R)-2-METHYLPIPERAZIN-1-YL]-2-OXIDANYLIDENE-BENZIMIDAZOL-5-YL]-2-METHOXY-BENZAMIDE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1LF11Ligand/IonN-[1,3-DIMETHYL-6-[(2R)-2-METHYLPIPERAZIN-1-YL]-2-OXIDANYLIDENE-BENZIMIDAZOL-5-YL]-2-METHOXY-BENZAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:651 , ILE A:652 , GLU A:655 , PRO A:656 , VAL A:657 , PRO A:658 , GLU A:661 , VAL A:662 , TYR A:707 , ASN A:708 , PHE A:714 , HOH A:2031 , HOH A:2085 , HOH A:2086 , GLU B:683 , ALA C:684 , TYR C:685 , HOH C:2052BINDING SITE FOR RESIDUE LF1 A1739
2AC2SOFTWARELYS A:639 , ASN B:651 , ILE B:652 , GLU B:655 , PRO B:656 , VAL B:657 , PRO B:658 , GLU B:661 , TYR B:707 , ASN B:708 , PHE B:714 , HOH B:2032 , HOH B:2046BINDING SITE FOR RESIDUE LF1 B1739
3AC3SOFTWAREASN C:651 , ILE C:652 , GLU C:655 , PRO C:656 , VAL C:657 , PRO C:658 , ASN C:708 , PHE C:714 , HOH C:2029 , HOH C:2036BINDING SITE FOR RESIDUE LF1 C1739
4AC4SOFTWAREALA B:684 , TYR B:685 , HOH B:2063 , HOH B:2065 , ARG C:638 , ASN D:651 , ILE D:652 , GLU D:655 , PRO D:656 , VAL D:657 , PRO D:658 , GLU D:661 , VAL D:662 , TYR D:707 , ASN D:708 , PHE D:714 , HOH D:2035 , HOH D:2086BINDING SITE FOR RESIDUE LF1 D1739

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G4R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5G4R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5G4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G4R)

(-) Exons   (0, 0)

(no "Exon" information available for 5G4R)

(-) 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:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 5g4r A 630 LTPFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEK 738
                                   639       649       659       669       679       689       699       709       719       729         


Chain B from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 5g4r B 627 EMQLTPFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEK 738
                                   636       646       656       666       676       686       696       706       716       726       736  


Chain C from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 5g4r C 627 EMQLTPFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEK 738
                                   636       646       656       666       676       686       696       706       716       726       736  


Chain D from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 5g4r D 630 LTPFLILLRKTLEQLQEKDTGNIFSEPVPLSEVPDYLDHIKKPMDFFTMKQNLEAYRYLNFDDFEEDFNLIVSNCLKYNAKDTIFYRAAVRLREQGGAVLRQARRQAEK 738
                                   639       649       659       669       679       689       699       709       719       729
   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 5G4R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G4R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G4R)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BRPF1_HUMAN | P55201: 2d9e 2rs9 2x35 2x4w 2x4x 2x4y 3l42 3mo8 4lc2 4qyd 4qyl 4uye 5c6s 5c7n 5c85 5c87 5c89 5d7x 5dy7 5dya 5dyc 5e3d 5e3g 5em3 5epr 5eps 5eq1 5erc 5etb 5etd 5ev9 5eva 5ewc 5ewd 5ewh 5ewv 5eww 5ffv 5ffw 5ffy 5fg4 5fg5 5g4s 5t4u 5t4v

(-) Related Entries Specified in the PDB File

5g4s BROMODOMAIN OF HUMAN BRPF1 WITH N-1,3-DIMETHYL-6- 2R-2-METHYLPIPERAZIN-1-YL-2-OXO-2,3-DIHYDRO-1H-1 ,3-BENZODIAZOL-5-YL-N-ETHYL-2-METHOXYBENZAMIDE