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Asym./Biol. Unit (Jmol Viewer)

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Title :   THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 3,5 DIMETHYLISOXAXOLE LIGAND

Authors :   C. Chung, O. Mirguet, Y. Lamotte, P. Bamborough, D. Delannee, A. Bouill F. Gellibert, G. Krysa, A. Lewis, J. Witherington, P. Huet, Y. Dudit, L E. Nicodeme

Date :   29 Jun 13 (Deposition) - 11 Sep 13 (Release) - 19 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Transcription, Inhibitor, Histone, Epigenetic Reader, Antagonist (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Mirguet, Y. Lamotte, C. Chung, P. Bamborough, D. Delannee, A. Bouillot, F. Gellibert, G. Krysa, A. Lewis, J. Witherington, P. Huet, Y. Dudit, L. Trottet, E. Nicodeme
Naphthyridines As Novel Bet Family Bromodomain Inhibitors.
Chemmedchem V. 9 589 2014
PubMed-ID: 24000170 | Reference-DOI: 10.1002/CMDC.201300259

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	N-TERMINAL BROMODOMAIN, RESIDUES 44-168
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BRD4, PROTEIN HUNK1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	9BM	1	Ligand/Ion	4-((2-(TERT-BUTYL)PHENYL)AMINO)-7-(3,5-DIMETHYLISOXAZOL-4-YL)-6-METHOXY-1,5-NAPHTHYRIDINE-3-CARBOXYLIC ACID
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	EDO A:1171 , HOH A:2085	BINDING SITE FOR RESIDUE EDO A1169
2	AC2	SOFTWARE	GLN A:64 , LYS A:155 , GLN A:159	BINDING SITE FOR RESIDUE EDO A1170
3	AC3	SOFTWARE	PRO A:86 , GLY A:108 , THR A:109 , LYS A:112 , EDO A:1169 , HOH A:2085	BINDING SITE FOR RESIDUE EDO A1171
4	AC4	SOFTWARE	SER A:51 , LYS A:57 , TRP A:81 , PRO A:82 , PHE A:83 , LEU A:92 , ASN A:116 , ASN A:140 , ILE A:146 , HOH A:2081 , HOH A:2110 , HOH A:2188 , HOH A:2189	BINDING SITE FOR RESIDUE 9BM A1172

(no "SS Bond" information available for 4BW3)

(no "Cis Peptide Bond" information available for 4BW3)

(no "SAP(SNP)/Variant" information available for 4BW3)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	BRD4_HUMAN	75-147 368-440	1	A:75-147 -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD4_HUMAN	80-139	1	A:80-139

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000263377	1	ENSE00001113198	chr19:15391262-15391075	188	BRD4_HUMAN	-	0	0	-	-
1.2	ENST00000263377	2	ENSE00001113202	chr19:15383944-15383626	319	BRD4_HUMAN	1-95	95	1	A:42-95	54
1.3	ENST00000263377	3	ENSE00000689046	chr19:15379853-15379716	138	BRD4_HUMAN	96-141	46	1	A:96-141	46
1.4	ENST00000263377	4	ENSE00000689047	chr19:15378362-15378227	136	BRD4_HUMAN	142-187	46	1	A:142-168	27
1.5	ENST00000263377	5	ENSE00000689048	chr19:15376454-15376165	290	BRD4_HUMAN	187-283	97	0	-	-
1.6	ENST00000263377	6	ENSE00000348853	chr19:15375577-15375215	363	BRD4_HUMAN	284-404	121	0	-	-
1.7	ENST00000263377	7	ENSE00000689050	chr19:15374359-15374231	129	BRD4_HUMAN	405-447	43	0	-	-
1.8	ENST00000263377	8	ENSE00000689051	chr19:15367984-15367775	210	BRD4_HUMAN	448-517	70	0	-	-
1.9	ENST00000263377	9	ENSE00000689052	chr19:15367074-15366875	200	BRD4_HUMAN	518-584	67	0	-	-
1.10	ENST00000263377	10	ENSE00000689053	chr19:15366403-15366108	296	BRD4_HUMAN	584-683	100	0	-	-
1.11	ENST00000263377	11	ENSE00001187704	chr19:15365073-15364963	111	BRD4_HUMAN	683-720	38	0	-	-
1.15	ENST00000263377	15	ENSE00001113203	chr19:15355573-15355521	53	BRD4_HUMAN	720-737	18	0	-	-
1.16	ENST00000263377	16	ENSE00001055985	chr19:15355411-15355042	370	BRD4_HUMAN	738-861	124	0	-	-
1.17	ENST00000263377	17	ENSE00001055976	chr19:15354298-15353711	588	BRD4_HUMAN	861-1057	197	0	-	-
1.18	ENST00000263377	18	ENSE00001136676	chr19:15350833-15350721	113	BRD4_HUMAN	1057-1094	38	0	-	-
1.19	ENST00000263377	19	ENSE00001113200	chr19:15350632-15350470	163	BRD4_HUMAN	1095-1149	55	0	-	-
1.20	ENST00000263377	20	ENSE00001113199	chr19:15350333-15350203	131	BRD4_HUMAN	1149-1192	44	0	-	-
1.21	ENST00000263377	21	ENSE00000951121	chr19:15350075-15349870	206	BRD4_HUMAN	1193-1261	69	0	-	-
1.22	ENST00000263377	22	ENSE00000951122	chr19:15349791-15349554	238	BRD4_HUMAN	1261-1340	80	0	-	-
1.23	ENST00000263377	23	ENSE00001055981	chr19:15349256-15348301	956	BRD4_HUMAN	1341-1362	22	0	-	-

Asymmetric/Biological 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:127
 aligned with BRD4_HUMAN | O60885 from UniProtKB/Swiss-Prot  Length:1362

    Alignment length:127
                                    51        61        71        81        91       101       111       121       131       141       151       161       
           BRD4_HUMAN    42 STNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEE 168
               SCOP domains d4bw3a_ A: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhh...hhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------BROMODOMAIN_2  PDB: A:75-147 UniProt: 75-147                             --------------------- PROSITE (1)
                PROSITE (2) --------------------------------------BROMODOMAIN_1  PDB: A:80-139 UniProt: 80-139                ----------------------------- PROSITE (2)
               Transcript 1 Exon 1.2  PDB: A:42-95 UniProt: 1-95 [INCOMPLETE]     Exon 1.3  PDB: A:96-141 UniProt: 96-141       Exon 1.4  PDB: A:142-168    Transcript 1
                 4bw3 A  42 SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEE 168
                                    51        61        71        81        91       101       111       121       131       141       151       161

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Bromodomain-like (339)

Superfamily: Bromodomain (203)

Family: automated matches (169)

Protein domain: automated matches (169)

Human (Homo sapiens) [TaxId: 9606] (162)

d4bw3a_

(no "CATH Domain" information available for 4BW3)

(no "Pfam Domain" information available for 4BW3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (BRD4_HUMAN | O60885)

molecular function
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0070577	lysine-acetylated histone binding	Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
	GO:0002039	p53 binding	Interacting selectively and non-covalently with one of the p53 family of proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:2000002	negative regulation of DNA damage checkpoint	Any process that stops, prevents, or reduces the frequency, rate or extent of a DNA damage checkpoint.
	GO:0010971	positive regulation of G2/M transition of mitotic cell cycle	Any process that increases the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0032968	positive regulation of transcription elongation from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0050727	regulation of inflammatory response	Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
	GO:1901407	regulation of phosphorylation of RNA polymerase II C-terminal domain	Any process that modulates the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain.
	GO:0000083	regulation of transcription involved in G1/S transition of mitotic cell cycle	Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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4bw1	THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 3,5 DIMETHYLISOXAXOLE LIGAND
4bw2	THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 3,5 DIMETHYLISOXAXOLE LIGAND
4bw4	THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 3,5 DIMETHYLISOXAXOLE LIGAND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (3, 3)

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SCOP Domains (1, 1)

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