3CXC

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

• PDB DOI: https://doi.org/10.2210/pdb3CXC/pdb
• NAKB: 3CXC

• Classification: RIBOSOME
• Organism(s): Haloarcula marismortui
• Mutation(s): No 


• Deposited: 2008-04-24 Released: 2009-04-28 
• Deposition Author(s): Ippolito, J.A., Wang, D., Kanyo, Z.F., Duffy, E.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.229 (Depositor) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 

Starting Model: experimental

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

• PubMed: 18947996 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 28-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1,459.56 kDa 
• Atom Count: 98,635 
• Modelled Residue Count: 6,580 
• Deposited Residue Count: 7,282 
• Unique protein chains: 28
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L2	D [auth A]	239	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P20276  Go to UniProtKB:  P20276

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L3	E [auth B]	337	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P20279  Go to UniProtKB:  P20279

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L4	F [auth C]	246	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12735  Go to UniProtKB:  P12735

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L5	G [auth D]	176	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14124  Go to UniProtKB:  P14124

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L6	H [auth E]	177	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14135  Go to UniProtKB:  P14135

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L7AE	I [auth F]	119	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12743  Go to UniProtKB:  P12743

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L10	J [auth G]	348	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P15825  Go to UniProtKB:  P15825

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L10E	K [auth H]	167	Haloarcula marismortui	Mutation(s): 0

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L13	L [auth I]	145	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P29198  Go to UniProtKB:  P29198

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L14	M [auth J]	132	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P22450  Go to UniProtKB:  P22450

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L15	N [auth K]	164	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12737  Go to UniProtKB:  P12737

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L15E	O [auth L]	194	Haloarcula marismortui	Mutation(s): 0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L18	P [auth M]	186	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14123  Go to UniProtKB:  P14123

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L18E	Q [auth N]	115	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12733  Go to UniProtKB:  P12733

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L19E	R [auth O]	148	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14119  Go to UniProtKB:  P14119

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L21E	S [auth P]	95	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12734  Go to UniProtKB:  P12734

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L22	T [auth Q]	154	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P10970  Go to UniProtKB:  P10970

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L23	U [auth R]	84	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12732  Go to UniProtKB:  P12732

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L24	V [auth S]	119	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P10972  Go to UniProtKB:  P10972

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L24E	W [auth T]	66	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14116  Go to UniProtKB:  P14116

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L29	X [auth U]	70	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P10971  Go to UniProtKB:  P10971

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L30	Y [auth V]	154	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P14121  Go to UniProtKB:  P14121

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L31E	Z [auth W]	91	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P18138  Go to UniProtKB:  P18138

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L32E	AA [auth X]	240	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P12736  Go to UniProtKB:  P12736

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L37AE	BA [auth Y]	73	Haloarcula marismortui	Mutation(s): 0

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L37E	CA [auth Z]	56	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P32410  Go to UniProtKB:  P32410

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L39E	DA [auth 1]	48	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P22452  Go to UniProtKB:  P22452

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN L44E	EA [auth 2]	92	Haloarcula marismortui	Mutation(s): 0
UniProt
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)) Explore P32411  Go to UniProtKB:  P32411

Entity ID: 1
Molecule	Chains	Length	Organism	Image
23S RIBOSOMAL RNA	A [auth 0]	2,922	Haloarcula marismortui

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5S RIBOSOMAL RNA	B [auth 9]	122	Haloarcula marismortui

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-R(*CP*CP*A)-3'	C [auth 4]	3	N/A

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SLD	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	AJ [auth Z], CJ [auth 2], NI [auth N], WI [auth T], ZI [auth Y]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
K	JE [auth 0], KE [auth 0]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	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	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	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.229 (Depositor) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.66	α = 90
b = 300.71	β = 90
c = 575.37	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-28 
Deposition Author(s): Ippolito, J.A., Wang, D., Kanyo, Z.F., Duffy, E.M.

Revision History  

• 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