4B3M

Crystal structure of the 30S ribosome in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics

Perez-Fernandez, D.Shcherbakov, D.Matt, T.Leong, N.C.Kudyba, I.Duscha, S.Boukari, H.Patak, R.Dubakka, S.R.Lang, K.Meyer, M.Akbergenov, R.Freihofer, P.Vaddi, S.Thommes, P.Ramakrishnan, V.Vasella, A.Bottger, E.C.

(2014) Nat Commun 5: 3112

  • DOI: https://doi.org/10.1038/ncomms4112
  • Primary Citation of Related Structures:  
    4B3M, 4B3R, 4B3S, 4B3T

  • PubMed Abstract: 

    Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.


  • Organizational Affiliation

    1] Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland [2].


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4208Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5161Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7155Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8138Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9128Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10104Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11129Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12132Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14 TYPE Z60Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1588Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1688Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17104Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1888Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1992Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20106Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXU [auth V]26Thermus thermophilus HB8Mutation(s): 0 
UniProt
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UniProt GroupQ5SIH3
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNA1,521Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
5'-R(*UP*UP*CP*AP*AP*AP)-3'V [auth W]6Thermus thermophilus HB8
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Entity ID: 23
MoleculeChains LengthOrganismImage
5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*CP)-3'W [auth Z]16Thermus thermophilus HB8
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ON0
Query on ON0

Download Ideal Coordinates CCD File 
PI [auth A](1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranoside
C30 H49 N5 O14
BJNRNAHKVYQUCR-CQXNUXSXSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FJ [auth D],
SJ [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
CF [auth A]
DF [auth A]
DJ [auth A]
EF [auth A]
FF [auth A]
CF [auth A],
DF [auth A],
DJ [auth A],
EF [auth A],
FF [auth A],
GF [auth A],
HF [auth A],
IF [auth A],
JF [auth A],
KF [auth A],
LF [auth A],
MF [auth A],
NF [auth A],
OF [auth A],
PF [auth A],
QF [auth A],
RF [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
AI [auth A],
AJ [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
BI [auth A],
BJ [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CG [auth A],
CH [auth A],
CI [auth A],
CJ [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DG [auth A],
DH [auth A],
DI [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EG [auth A],
EH [auth A],
EI [auth A],
EJ [auth B],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FG [auth A],
FH [auth A],
FI [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GG [auth A],
GH [auth A],
GI [auth A],
GJ [auth D],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HG [auth A],
HH [auth A],
HI [auth A],
HJ [auth E],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IG [auth A],
IH [auth A],
II [auth A],
IJ [auth E],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JG [auth A],
JH [auth A],
JI [auth A],
JJ [auth E],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KG [auth A],
KH [auth A],
KI [auth A],
KJ [auth H],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LG [auth A],
LH [auth A],
LI [auth A],
LJ [auth H],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MG [auth A],
MH [auth A],
MI [auth A],
MJ [auth H],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NG [auth A],
NH [auth A],
NI [auth A],
NJ [auth H],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OG [auth A],
OH [auth A],
OI [auth A],
OJ [auth I],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PG [auth A],
PH [auth A],
PJ [auth K],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QG [auth A],
QH [auth A],
QI [auth A],
QJ [auth L],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RG [auth A],
RH [auth A],
RI [auth A],
RJ [auth M],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
SH [auth A],
SI [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth A],
TH [auth A],
TI [auth A],
TJ [auth N],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
UH [auth A],
UI [auth A],
UJ [auth Q],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
VH [auth A],
VI [auth A],
VJ [auth T],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
WH [auth A],
WI [auth A],
WJ [auth Z],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
XH [auth A],
XI [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YH [auth A],
YI [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A],
ZH [auth A],
ZI [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 401.65α = 90
b = 401.65β = 90
c = 175.26γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Other, Structure summary
  • Version 1.2: 2014-01-29
    Changes: Database references
  • Version 1.3: 2014-02-12
    Changes: Database references
  • Version 1.4: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.5: 2019-03-06
    Changes: Data collection, Experimental preparation
  • Version 1.6: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description