4HYP - JenaLib

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Biological Unit 6 (Jmol Viewer)

Title :   PYRROLOPYRIMIDINE INHIBITORS OF DNA GYRASE B AND TOPOISOMERASE IV, PART I: STRUCTURE GUIDED DISCOVERY AND OPTIMIZATION OF DUAL TARGETING AGENTS WITH POTENT, BROAD-SPECTRUM ENZYMATIC ACTIVITY.

Authors :   D. C. Bensen, C. J. Creighton, L. W. Tari

Date :   13 Nov 12 (Deposition) - 13 Feb 13 (Release) - 27 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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)
Biol. Unit 5: A,B  (1x)
Biol. Unit 6: C,D  (1x)

Keywords :   Gyrase, Gyrb, Atp-Binding, Nucleotide-Binding, Topoisomerase, Atp- Binding Domain, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. W. Tari, M. Trzoss, D. C. Bensen, X. Li, Z. Chen, T. Lam, J. Zhang, C. J. Creighton, M. L. Cunningham, B. Kwan, M. Stidham, K. J. Shaw, F. C. Lightstone, S. E. Wong, T. B. Nguyen, J. Nix, J. Finn
Pyrrolopyrimidine Inhibitors Of Dna Gyrase B (Gyrb) And Topoisomerase Iv (Pare). Part I: Structure Guided Discovery And Optimization Of Dual Targeting Agents With Potent, Broad-Spectrum Enzymatic Activity.
Bioorg. Med. Chem. Lett. V. 23 1529 2013
PubMed-ID: 23352267 | Reference-DOI: 10.1016/J.BMCL.2012.11.032

Molecule 1 - DNA GYRASE SUBUNIT B
	Chains	:	A, B, C, D
	EC Number	:	5.99.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	ACRB, B3699, GYRB, HIMB, HISU, JW5625, NALC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:	A	B
Biological Unit 6 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	1A1	4	Ligand/Ion	N-[7-(1H-IMIDAZOL-1-YL)-2-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-D]PYRIMIDIN-5-YL]CYCLOPROPANECARBOXAMIDE
2	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	1A1	1	Ligand/Ion	N-[7-(1H-IMIDAZOL-1-YL)-2-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-D]PYRIMIDIN-5-YL]CYCLOPROPANECARBOXAMIDE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	1A1	1	Ligand/Ion	N-[7-(1H-IMIDAZOL-1-YL)-2-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-D]PYRIMIDIN-5-YL]CYCLOPROPANECARBOXAMIDE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	1A1	1	Ligand/Ion	N-[7-(1H-IMIDAZOL-1-YL)-2-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-D]PYRIMIDIN-5-YL]CYCLOPROPANECARBOXAMIDE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	1A1	1	Ligand/Ion	N-[7-(1H-IMIDAZOL-1-YL)-2-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-D]PYRIMIDIN-5-YL]CYCLOPROPANECARBOXAMIDE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 5 (1, 2)

No.	Name	Count	Type	Full Name
1	1A1	2	Ligand/Ion	N-[7-(1H-IMIDAZOL-1-YL)-2-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-D]PYRIMIDIN-5-YL]CYCLOPROPANECARBOXAMIDE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 6 (1, 2)

No.	Name	Count	Type	Full Name
1	1A1	2	Ligand/Ion	N-[7-(1H-IMIDAZOL-1-YL)-2-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-D]PYRIMIDIN-5-YL]CYCLOPROPANECARBOXAMIDE
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:43 , ASN A:46 , GLU A:50 , VAL A:71 , ASP A:73 , ARG A:76 , GLY A:77 , ILE A:78 , PRO A:79 , ILE A:94 , PHE A:104 , ARG A:140 , THR A:169 , HOH A:426 , HOH A:436	BINDING SITE FOR RESIDUE 1A1 A 301
2	AC2	SOFTWARE	GLU A:42 , ASP A:45 , GLY A:118 , LEU A:119 , VAL A:122 , HOH A:465	BINDING SITE FOR RESIDUE MG A 302
3	AC3	SOFTWARE	VAL B:43 , ASN B:46 , ALA B:47 , GLU B:50 , VAL B:71 , ASP B:73 , ARG B:76 , GLY B:77 , ILE B:78 , PRO B:79 , ILE B:94 , PHE B:104 , ARG B:140 , THR B:169 , HOH B:420 , HOH B:440 , HOH B:479	BINDING SITE FOR RESIDUE 1A1 B 301
4	AC4	SOFTWARE	GLU B:42 , ASP B:45 , VAL B:122 , HOH B:472 , HOH B:473	BINDING SITE FOR RESIDUE MG B 302
5	AC5	SOFTWARE	VAL C:43 , ASN C:46 , GLU C:50 , VAL C:71 , ASP C:73 , ARG C:76 , GLY C:77 , ILE C:78 , PRO C:79 , ILE C:94 , PHE C:104 , ARG C:140 , THR C:169 , HOH C:416 , HOH C:428 , HOH C:437 , HOH C:478	BINDING SITE FOR RESIDUE 1A1 C 301
6	AC6	SOFTWARE	GLU C:42 , ASP C:45 , LEU C:119 , VAL C:122 , HOH C:477	BINDING SITE FOR RESIDUE MG C 302
7	AC7	SOFTWARE	VAL D:43 , ASN D:46 , ALA D:47 , GLU D:50 , ASP D:73 , ARG D:76 , ILE D:78 , PRO D:79 , ARG D:140 , THR D:169 , HOH D:402 , HOH D:407 , HOH D:441 , HOH D:456	BINDING SITE FOR RESIDUE 1A1 D 301
8	AC8	SOFTWARE	GLU D:42 , ASP D:45 , VAL D:122 , HOH D:472	BINDING SITE FOR RESIDUE MG D 302

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

Asymmetric Unit

No.	Residues
1	Ser B:116	-	Gly B:117
2	Ser C:116	-	Gly C:117

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

(no "PROSITE Motif" information available for 4HYP)

(no "Exon" information available for 4HYP)

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:194
                                                                                                                                                                                                                                  
               SCOP domains d4hypa_ A: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee....................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hyp A  15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIVSAAEVIMTVLHAGGKFKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY 222
                                    24        34        44        54        64        74       |89        99    || 118       128       138       148       158       168       178       188       198       208       218    
                                                                                              82|             104|                                                                                                            
                                                                                               88              114

Chain B from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains d4hypb_ B: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee....................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hyp B  15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIVSAAEVIMTVLHAGGKFKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY 222
                                    24        34        44        54        64        74       |89        99    || 118       128       138       148       158       168       178       188       198       208       218    
                                                                                              82|             104|                                                                                                            
                                                                                               88              114

Chain C from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains d4hypc_ C: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee....................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hyp C  15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIVSAAEVIMTVLHAGGKFKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY 222
                                    24        34        44        54        64        74       |89        99    || 118       128       138       148       158       168       178       188       198       208       218    
                                                                                              82|             104|                                                                                                            
                                                                                               88              114

Chain D from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains d4hypd_ D: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee....................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hyp D  15 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIVSAAEVIMTVLHAGGKFKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY 222
                                    24        34        44        54        64        74       |89        99    || 118       128       138       148       158       168       178       188       198       208       218    
                                                                                              82|             104|                                                                                                            
                                                                                               88              114

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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 '\|'

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

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

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	Cis Peptide Bonds
		Ser B:116 - Gly B:117	[ RasMol ]
		Ser C:116 - Gly C:117	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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