ISDA

Deposition Date 2008-04-24

Release Date 2009-04-28

Last Version Date 2023-08-30

Entry Detail

PDB ID:

3CXC

Keywords:

RIBOSOME

Title:

The structure of an enhanced oxazolidinone inhibitor bound to the 50S ribosomal subunit of H. marismortui

Biological Source:

Source Organism:

Haloarcula marismortui (Taxon ID: 2238)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.00 Å

R-Value Free:

0.22

R-Value Work:

0.18

Space Group:

C 2 2 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:23S RIBOSOMAL RNA
Chain IDs:A (auth: 0)
Chain Length:2922
Number of Molecules:1
Biological Source:Haloarcula marismortui

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L39E
Gene (Uniprot):rpl39e
Chain IDs:DA (auth: 1)
Chain Length:48
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P22452 Pfam ID:PF00832

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L44E
Gene (Uniprot):rpl44e
Chain IDs:EA (auth: 2)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P32411 Pfam ID:PF00935

Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:B (auth: 9)
Chain Length:122
Number of Molecules:1
Biological Source:Haloarcula marismortui

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L2
Gene (Uniprot):rpl2
Chain IDs:D (auth: A)
Chain Length:239
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P20276 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L3
Gene (Uniprot):rpl3
Chain IDs:E (auth: B)
Chain Length:337
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P20279 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L4
Gene (Uniprot):rpl4
Chain IDs:F (auth: C)
Chain Length:246
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12735 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L5
Gene (Uniprot):rpl5
Chain IDs:G (auth: D)
Chain Length:176
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14124 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L6
Gene (Uniprot):rpl6
Chain IDs:H (auth: E)
Chain Length:177
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14135 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L7AE
Gene (Uniprot):rpl7ae
Chain IDs:I (auth: F)
Chain Length:119
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12743 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L10
Gene (Uniprot):rpl10
Chain IDs:J (auth: G)
Chain Length:348
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P15825 Pfam ID:PF00466, PF17777

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L10E
Chain IDs:K (auth: H)
Chain Length:167
Number of Molecules:1
Biological Source:Haloarcula marismortui

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L13
Gene (Uniprot):rpl13
Chain IDs:L (auth: I)
Chain Length:145
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P29198 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L14
Gene (Uniprot):rpl14
Chain IDs:M (auth: J)
Chain Length:132
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P22450 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L15
Gene (Uniprot):rpl15
Chain IDs:N (auth: K)
Chain Length:164
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12737 Pfam ID:PF00828

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L15E
Chain IDs:O (auth: L)
Chain Length:194
Number of Molecules:1
Biological Source:Haloarcula marismortui

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L18
Gene (Uniprot):rpl18
Chain IDs:P (auth: M)
Chain Length:186
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14123 Pfam ID:PF17144

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L18E
Gene (Uniprot):rpl18e
Chain IDs:Q (auth: N)
Chain Length:115
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12733 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L19E
Gene (Uniprot):rpl19e
Chain IDs:R (auth: O)
Chain Length:148
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14119 Pfam ID:PF01280

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L21E
Gene (Uniprot):rpl21e
Chain IDs:S (auth: P)
Chain Length:95
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12734 Pfam ID:PF01157

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L22
Gene (Uniprot):rpl22
Chain IDs:T (auth: Q)
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P10970 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L23
Gene (Uniprot):rpl23
Chain IDs:U (auth: R)
Chain Length:84
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12732 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L24
Gene (Uniprot):rpl24
Chain IDs:V (auth: S)
Chain Length:119
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P10972 Pfam ID:PF16906, PF00467

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L24E
Gene (Uniprot):rpl24e
Chain IDs:W (auth: T)
Chain Length:66
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14116 Pfam ID:PF01246

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L29
Gene (Uniprot):rpl29
Chain IDs:X (auth: U)
Chain Length:70
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P10971 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L30
Gene (Uniprot):rpl30
Chain IDs:Y (auth: V)
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P14121 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L31E
Gene (Uniprot):rpl31e
Chain IDs:Z (auth: W)
Chain Length:91
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P18138 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L32E
Gene (Uniprot):rpl32e
Chain IDs:AA (auth: X)
Chain Length:240
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P12736 Pfam ID:PF14520, PF01655

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L37AE
Chain IDs:BA (auth: Y)
Chain Length:73
Number of Molecules:1
Biological Source:Haloarcula marismortui

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RIBOSOMAL PROTEIN L37E
Gene (Uniprot):rpl37e
Chain IDs:CA (auth: Z)
Chain Length:56
Number of Molecules:1
Biological Source:Haloarcula marismortui

UniProt ID:P32410 Pfam ID:PF01907

Ligand Molecules

SLD

Primary Citation

Design at the atomic level: design of biaryloxazolidinones as potent orally active antibiotics.

Zhou, J, Bhattacharjee, A, Chen, S, Chen, Y, Duffy, E, Farmer, J, Goldberg, J, Hanselmann, R, Ippolito, J.A, Lou, R, Orbin, A, Oyelere, A, Salvino, J, Springer, D, Tran, J, Wang, D, Wu, Y, Johnson, G.Show

Bioorg.Med.Chem.Lett. 18 6175 6178 (2008)

PMID: 18947996 DOI: 10.1016/j.bmcl.2008.10.011

Abstact

We have developed a first generation of hybrid sparsomycin-linezolid compounds into a new family of orally bioavailable biaryloxazolidinones that have activity against both linezolid-susceptible and -resistant gram-positive bacteria as well as the fastidious gram-negative bacteria Haemophilus influenzae and Moraxella catarrahalis. The convergent synthesis of these new compounds is detailed.

Legend

Protein

Chemical

Disease

Primary Citation of related structures