4A9F - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-METHYLPYRROLIDIN-2-ONE

Authors :   C. W. Chung, P. Bamborough

Date :   26 Nov 11 (Deposition) - 11 Jan 12 (Release) - 08 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

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

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

Reference :   C. W. Chung, A. W. Dean, J. M. Woolven, P. Bamborough
Fragment-Based Discovery Of Bromodomain Inhibitors Part 1: Inhibitor Binding Modes And Implications For Lead Discovery.
J. Med. Chem. V. 55 576 2012
PubMed-ID: 22136404 | Reference-DOI: 10.1021/JM201320W

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 2
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	N-TERMINAL BROMODOMAIN (BD1), RESIDUES 67-200
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HUMAN BRD2

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MB3	3	Ligand/Ion	1-METHYLPYRROLIDIN-2-ONE
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MB3	2	Ligand/Ion	1-METHYLPYRROLIDIN-2-ONE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	MB3	2	Ligand/Ion	1-METHYLPYRROLIDIN-2-ONE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:128 , ARG B:129 , HOH B:2077	BINDING SITE FOR RESIDUE EDO B1186
2	AC2	SOFTWARE	PHE A:99 , VAL A:103 , LEU A:108 , ASN A:156 , HOH A:2079	BINDING SITE FOR RESIDUE MB3 A1183
3	AC3	SOFTWARE	PHE B:99 , VAL B:103 , ASN B:156 , HOH B:2051	BINDING SITE FOR RESIDUE MB3 B1187
4	AC4	SOFTWARE	VAL C:103 , LEU C:108 , ASN C:156 , HOH C:2045	BINDING SITE FOR RESIDUE MB3 C1183
5	AC5	SOFTWARE	ARG B:100 , ARG C:128 , ASN C:132 , TYR C:134 , HOH C:2068 , HOH C:2112	BINDING SITE FOR RESIDUE SO4 C1184
6	AC6	SOFTWARE	ARG A:100 , HOH A:2021 , HOH A:2024 , HOH A:2200 , HOH A:2202	BINDING SITE FOR RESIDUE SO4 A1184

(no "SS Bond" information available for 4A9F)

(no "Cis Peptide Bond" information available for 4A9F)

(no "SAP(SNP)/Variant" information available for 4A9F)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	BRD2_HUMAN	91-163 364-436	3	A:91-163 B:91-163 C:91-163 -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD2_HUMAN	96-155 369-428	3	A:96-155 B:96-155 C:96-155 -

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	BRD2_HUMAN	91-163 364-436	2	A:91-163 B:91-163 - -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD2_HUMAN	96-155 369-428	2	A:96-155 B:96-155 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	BRD2_HUMAN	91-163 364-436	2	- - C:91-163 -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD2_HUMAN	96-155 369-428	2	- - C:96-155 -

Asymmetric Unit (3, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.7b	ENST00000399529	7b	ENSE00001705137	HSCHR6_MHC_QBL:32865184-32865580	397	BRD2_HUMAN	-	0	0	-	-
1.13b	ENST00000399529	13b	ENSE00002152230	HSCHR6_MHC_QBL:32868119-32869451	1333	BRD2_HUMAN	1-10	10	0	-	-
1.16e	ENST00000399529	16e	ENSE00001730437	HSCHR6_MHC_QBL:32870986-32871289	304	BRD2_HUMAN	10-111	102	3	A:75-111 B:76-111 C:76-111	37 36 36
1.17	ENST00000399529	17	ENSE00001742408	HSCHR6_MHC_QBL:32871904-32872041	138	BRD2_HUMAN	112-157	46	3	A:112-157 B:112-157 C:112-157	46 46 46
1.18a	ENST00000399529	18a	ENSE00001669691	HSCHR6_MHC_QBL:32872548-32872686	139	BRD2_HUMAN	158-204	47	3	A:158-182 B:158-185 C:158-182	25 28 25
1.19	ENST00000399529	19	ENSE00001606367	HSCHR6_MHC_QBL:32872768-32872982	215	BRD2_HUMAN	204-275	72	0	-	-
1.20b	ENST00000399529	20b	ENSE00002150037	HSCHR6_MHC_QBL:32873080-32873454	375	BRD2_HUMAN	276-400	125	0	-	-
1.20g	ENST00000399529	20g	ENSE00001741071	HSCHR6_MHC_QBL:32873960-32874088	129	BRD2_HUMAN	401-443	43	0	-	-
1.21b	ENST00000399529	21b	ENSE00001731564	HSCHR6_MHC_QBL:32874275-32874523	249	BRD2_HUMAN	444-526	83	0	-	-
1.22c	ENST00000399529	22c	ENSE00001594402	HSCHR6_MHC_QBL:32874644-32874906	263	BRD2_HUMAN	527-614	88	0	-	-
1.24c	ENST00000399529	24c	ENSE00001800691	HSCHR6_MHC_QBL:32876345-32876649	305	BRD2_HUMAN	614-716	103	0	-	-
1.24d	ENST00000399529	24d	ENSE00001781532	HSCHR6_MHC_QBL:32876859-32876981	123	BRD2_HUMAN	716-757	42	0	-	-
1.25d	ENST00000399529	25d	ENSE00001732199	HSCHR6_MHC_QBL:32877099-32878022	924	BRD2_HUMAN	757-801	45	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:108
 aligned with BRD2_HUMAN | P25440 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:108
                                    84        94       104       114       124       134       144       154       164       174        
           BRD2_HUMAN    75 VTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQ 182
               SCOP domains d4a9fa_ A: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------BROMODOMAIN_2  PDB: A:91-163 UniProt: 91-163                             ------------------- PROSITE (1)
                PROSITE (2) ---------------------BROMODOMAIN_1  PDB: A:96-155 UniProt: 96-155                --------------------------- PROSITE (2)
               Transcript 1 Exon 1.16e  PDB: A:75-111            Exon 1.17  PDB: A:112-157 UniProt: 112-157    Exon 1.18a  PDB: A:158-18 Transcript 1
                 4a9f A  75 VTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQ 182
                                    84        94       104       114       124       134       144       154       164       174

Chain B from PDB  Type:PROTEIN  Length:110
 aligned with BRD2_HUMAN | P25440 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:110
                                    85        95       105       115       125       135       145       155       165       175       185
           BRD2_HUMAN    76 TNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQ 185
               SCOP domains d4a9fb_ B: 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: B:91-163 UniProt: 91-163                             ---------------------- PROSITE (1)
                PROSITE (2) --------------------BROMODOMAIN_1  PDB: B:96-155 UniProt: 96-155                ------------------------------ PROSITE (2)
               Transcript 1 Exon 1.16e  PDB: B:76-111           Exon 1.17  PDB: B:112-157 UniProt: 112-157    Exon 1.18a  PDB: B:158-185   Transcript 1
                 4a9f B  76 TNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQ 185
                                    85        95       105       115       125       135       145       155       165       175       185

Chain C from PDB  Type:PROTEIN  Length:107
 aligned with BRD2_HUMAN | P25440 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:107
                                    85        95       105       115       125       135       145       155       165       175       
           BRD2_HUMAN    76 TNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQ 182
               SCOP domains d4a9fc_ C: 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: C:91-163 UniProt: 91-163                             ------------------- PROSITE (1)
                PROSITE (2) --------------------BROMODOMAIN_1  PDB: C:96-155 UniProt: 96-155                --------------------------- PROSITE (2)
               Transcript 1 Exon 1.16e  PDB: C:76-111           Exon 1.17  PDB: C:112-157 UniProt: 112-157    Exon 1.18a  PDB: C:158-18 Transcript 1
                 4a9f C  76 TNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQ 182
                                    85        95       105       115       125       135       145       155       165       175

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

1a	d4a9fa_	A:
1b	d4a9fb_	B:
1c	d4a9fc_	C:

(no "CATH Domain" information available for 4A9F)

(no "Pfam Domain" information available for 4A9F)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (BRD2_HUMAN | P25440)

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: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:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

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	4a9f
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1x0j	CRYSTAL STRUCTURE ANALYSIS OF THE N-TERMINAL BROMODOMAIN OFHUMAN BRD2
2ydw	CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD2 WITH THE INHIBITOR GW841819X
2yek	CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD2 WITH THE INHIBITOR GSK525762 (IBET)
4a9e	N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 3-METHYL-1 ,2,3,4-TETRAHYDROQUINAZOLIN-2-ONE
4a9h	N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-(2- METHYL-1,2,3,4-TETRAHYDROQUINOLIN-1-YL)ETHAN-1-ONE
4a9i	N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 3-METHYL-1 ,2,3,4-TETRAHYDROQUINAZOLIN-2-ONE
4a9j	N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N-(4- HYDROXYPHENYL)ACETAMIDE
4a9k	BROMODOMAIN OF HUMAN CREBBP WITH N-(4-HYDROXYPHENYL) ACETAMIDE
4a9l	N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1,3- DIMETHYL-6-(MORPHOLINE-4-SULFONYL)-1,2,3,4- TETRAHYDROQUINAZOLIN-2-ONE
4a9m	N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N- CYCLOPENTYL-5-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-2- METHYLBENZENE-1-SULFONAMIDE
4a9n	N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N- CYCLOPROPYL-5-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-2- METHYLBENZENE-1-SULFONAMIDE
4a9o	N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 5 ETHYL-3 -METHYL-4-PHENYL-1,2-OXAZOLE
4a9p	N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 3,5 DIMETHYL-4-PHENYL-1,2-OXAZOLE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Exons (3, 9)

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SCOP Domains (1, 3)

CATH Domains (0, 0)

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Gene Ontology (10, 10)

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