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 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmcl.2008.10.011
  • Primary Citation of Related Structures:  
    3CXC

  • 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 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
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L2D [auth A]239Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L3E [auth B]337Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L4F [auth C]246Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L5G [auth D]176Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L6H [auth E]177Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L7AEI [auth F]119Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10J [auth G]348Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L10EK [auth H]167Haloarcula marismortuiMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L13L [auth I]145Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L14M [auth J]132Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15N [auth K]164Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15EO [auth L]194Haloarcula marismortuiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18P [auth M]186Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L18EQ [auth N]115Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L19ER [auth O]148Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L21ES [auth P]95Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L22T [auth Q]154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L23U [auth R]84Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24V [auth S]119Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L24EW [auth T]66Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L29X [auth U]70Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L30Y [auth V]154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L31EZ [auth W]91Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L32EAA [auth X]240Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37AEBA [auth Y]73Haloarcula marismortuiMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37ECA [auth Z]56Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L39EDA [auth 1]48Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L44EEA [auth 2]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNAA [auth 0]2,922Haloarcula marismortui
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAB [auth 9]122Haloarcula marismortui
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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-R(*CP*CP*A)-3'C [auth 4]3N/A
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SLD
Query on SLD
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FA [auth 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
CD
Query on CD
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AJ [auth Z],
CJ [auth 2],
NI [auth N],
WI [auth T],
ZI [auth Y]		CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
K
Query on K
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JE [auth 0],
KE [auth 0]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL
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DI [auth I]
DJ [auth 2]
EI [auth I]
FI [auth I]
GH [auth 0]
DI [auth I],
DJ [auth 2],
EI [auth I],
FI [auth I],
GH [auth 0],
HH [auth 0],
HI [auth J],
IH [auth 0],
JH [auth 0],
JI [auth K],
KH [auth 0],
LH [auth 0],
LI [auth L],
MH [auth 0],
MI [auth M],
NH [auth 0],
OI [auth N],
QI [auth P],
TI [auth Q],
WH [auth A],
YH [auth B],
YI [auth X]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
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AB [auth 0]
AC [auth 0]
AD [auth 0]
AE [auth 0]
BB [auth 0]
AB [auth 0],
AC [auth 0],
AD [auth 0],
AE [auth 0],
BB [auth 0],
BC [auth 0],
BD [auth 0],
BE [auth 0],
BJ [auth 2],
CB [auth 0],
CC [auth 0],
CD [auth 0],
CE [auth 0],
DB [auth 0],
DC [auth 0],
DD [auth 0],
DE [auth 0],
EB [auth 0],
EC [auth 0],
ED [auth 0],
EE [auth 0],
FB [auth 0],
FC [auth 0],
FD [auth 0],
FE [auth 0],
GA [auth 0],
GB [auth 0],
GC [auth 0],
GD [auth 0],
GE [auth 0],
GI [auth J],
HA [auth 0],
HB [auth 0],
HC [auth 0],
HD [auth 0],
HE [auth 0],
IA [auth 0],
IB [auth 0],
IC [auth 0],
ID [auth 0],
IE [auth 0],
JA [auth 0],
JB [auth 0],
JC [auth 0],
JD [auth 0],
KA [auth 0],
KB [auth 0],
KC [auth 0],
KD [auth 0],
LA [auth 0],
LB [auth 0],
LC [auth 0],
LD [auth 0],
MA [auth 0],
MB [auth 0],
MC [auth 0],
MD [auth 0],
NA [auth 0],
NB [auth 0],
NC [auth 0],
ND [auth 0],
OA [auth 0],
OB [auth 0],
OC [auth 0],
OD [auth 0],
OH [auth 9],
PA [auth 0],
PB [auth 0],
PC [auth 0],
PD [auth 0],
PH [auth 9],
QA [auth 0],
QB [auth 0],
QC [auth 0],
QD [auth 0],
RA [auth 0],
RB [auth 0],
RC [auth 0],
RD [auth 0],
SA [auth 0],
SB [auth 0],
SC [auth 0],
SD [auth 0],
SH [auth 4],
TA [auth 0],
TB [auth 0],
TC [auth 0],
TD [auth 0],
TH [auth A],
UA [auth 0],
UB [auth 0],
UC [auth 0],
UD [auth 0],
UH [auth A],
VA [auth 0],
VB [auth 0],
VC [auth 0],
VD [auth 0],
VI [auth S],
WA [auth 0],
WB [auth 0],
WC [auth 0],
WD [auth 0],
XA [auth 0],
XB [auth 0],
XC [auth 0],
XD [auth 0],
XH [auth B],
XI [auth X],
YA [auth 0],
YB [auth 0],
YC [auth 0],
YD [auth 0],
ZA [auth 0],
ZB [auth 0],
ZC [auth 0],
ZD [auth 0]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
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AF [auth 0]
AG [auth 0]
AH [auth 0]
AI [auth H]
BF [auth 0]
AF [auth 0],
AG [auth 0],
AH [auth 0],
AI [auth H],
BF [auth 0],
BG [auth 0],
BH [auth 0],
BI [auth H],
CF [auth 0],
CG [auth 0],
CH [auth 0],
CI [auth I],
DF [auth 0],
DG [auth 0],
DH [auth 0],
EF [auth 0],
EG [auth 0],
EH [auth 0],
FF [auth 0],
FG [auth 0],
FH [auth 0],
GF [auth 0],
GG [auth 0],
HF [auth 0],
HG [auth 0],
IF [auth 0],
IG [auth 0],
II [auth K],
JF [auth 0],
JG [auth 0],
KF [auth 0],
KG [auth 0],
KI [auth L],
LE [auth 0],
LF [auth 0],
LG [auth 0],
ME [auth 0],
MF [auth 0],
MG [auth 0],
NE [auth 0],
NF [auth 0],
NG [auth 0],
OE [auth 0],
OF [auth 0],
OG [auth 0],
PE [auth 0],
PF [auth 0],
PG [auth 0],
PI [auth P],
QE [auth 0],
QF [auth 0],
QG [auth 0],
QH [auth 9],
RE [auth 0],
RF [auth 0],
RG [auth 0],
RH [auth 9],
RI [auth Q],
SE [auth 0],
SF [auth 0],
SG [auth 0],
SI [auth Q],
TE [auth 0],
TF [auth 0],
TG [auth 0],
UE [auth 0],
UF [auth 0],
UG [auth 0],
UI [auth R],
VE [auth 0],
VF [auth 0],
VG [auth 0],
VH [auth A],
WE [auth 0],
WF [auth 0],
WG [auth 0],
XE [auth 0],
XF [auth 0],
XG [auth 0],
YE [auth 0],
YF [auth 0],
YG [auth 0],
ZE [auth 0],
ZF [auth 0],
ZG [auth 0],
ZH [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SLD PDBBind:  3CXC IC50: 4600 (nM) from 1 assay(s)
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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Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description