3CXC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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.

(2008) Bioorg Med Chem Lett 18: 6175-6178

  • DOI: 10.1016/j.bmcl.2008.10.011
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 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 fa ...

    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.


    Organizational Affiliation

    Department of Medicinal Chemistry, Rib-X Pharmaceuticals Inc., 300 George Street, Suite 301, New Haven, CT 06511, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L2A239Haloarcula marismortuiMutation(s): 0 
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L3B337Haloarcula marismortuiMutation(s): 0 
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L4C246Haloarcula marismortuiMutation(s): 0 
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L5D176Haloarcula marismortuiMutation(s): 0 
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L6E177Haloarcula marismortuiMutation(s): 0 
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L7AEF119Haloarcula marismortuiMutation(s): 0 
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L10G348Haloarcula marismortuiMutation(s): 0 
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L10EH167Haloarcula marismortuiMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L13I145Haloarcula marismortuiMutation(s): 0 
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L14J132Haloarcula marismortuiMutation(s): 0 
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L15K164Haloarcula marismortuiMutation(s): 0 
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L15EL194Haloarcula marismortuiMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L18M186Haloarcula marismortuiMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L18EN115Haloarcula marismortuiMutation(s): 0 
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L19EO148Haloarcula marismortuiMutation(s): 0 
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L21EP95Haloarcula marismortuiMutation(s): 0 
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L22Q154Haloarcula marismortuiMutation(s): 0 
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L23R84Haloarcula marismortuiMutation(s): 0 
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L24S119Haloarcula marismortuiMutation(s): 0 
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L24ET66Haloarcula marismortuiMutation(s): 0 
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L29U70Haloarcula marismortuiMutation(s): 0 
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L30V154Haloarcula marismortuiMutation(s): 0 
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L31EW91Haloarcula marismortuiMutation(s): 0 
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L32EX240Haloarcula marismortuiMutation(s): 0 
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L37AEY73Haloarcula marismortuiMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L37EZ56Haloarcula marismortuiMutation(s): 0 
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L39E148Haloarcula marismortuiMutation(s): 0 
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN L44E292Haloarcula marismortuiMutation(s): 0 
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNA02922Haloarcula marismortui

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Entity ID: 2
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNA9122Haloarcula marismortui
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Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*CP*CP*A)-3'43N/A
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SLD
Query on SLD

Download CCD File 
0
(3Z)-N-[(4E)-5-(4-{(5S)-5-[(acetylamino)methyl]-2-oxo-1,3-oxazolidin-3-yl}-2-fluorophenyl)pent-4-en-1-yl]-3-(4-methyl-2,6-dioxo-1,6-dihydropyrimidin-5(2H)-ylidene)propanamide
C25 H28 F N5 O6
UDBPSKMSYCUBIU-MTQXBESRSA-N
 Ligand Interaction
CD
Query on CD

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2, N, T, Y, Z
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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0
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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0, 2, A, B, I, J, K, L, M, N, P, Q, X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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0, 2, 4, 9, A, B, J, S, X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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0, 9, A, C, H, I, K, L, P, Q, R
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SLDIC50 :  4600   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.66α = 90
b = 300.71β = 90
c = 575.37γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
CNXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance