4GKH

Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor 1-NA-PP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance.

Stogios, P.J.Spanogiannopoulos, P.Evdokimova, E.Egorova, O.Shakya, T.Todorovic, N.Capretta, A.Wright, G.D.Savchenko, A.

(2013) Biochem J 454: 191-200

  • DOI: 10.1042/BJ20130317
  • Primary Citation of Related Structures:  
    4EJ7, 4FEU, 4FEV, 4FEW, 4FEX, 4GKH, 4GKI

  • PubMed Abstract: 
  • Activity of the aminoglycoside phosphotransferase APH(3')-Ia leads to resistance to aminoglycoside antibiotics in pathogenic Gram-negative bacteria, and contributes to the clinical obsolescence of this class of antibiotics. One strategy to rescue compromised antibiotics such as aminoglycosides is targeting the enzymes that confer resistance with small molecules ...

    Activity of the aminoglycoside phosphotransferase APH(3')-Ia leads to resistance to aminoglycoside antibiotics in pathogenic Gram-negative bacteria, and contributes to the clinical obsolescence of this class of antibiotics. One strategy to rescue compromised antibiotics such as aminoglycosides is targeting the enzymes that confer resistance with small molecules. We demonstrated previously that ePK (eukaryotic protein kinase) inhibitors could inhibit APH enzymes, owing to the structural similarity between these two enzyme families. However, limited structural information of enzyme-inhibitor complexes hindered interpretation of the results. In addition, cross-reactivity of compounds between APHs and ePKs represents an obstacle to their use as aminoglycoside adjuvants to rescue aminoglycoside antibiotic activity. In the present study, we structurally and functionally characterize inhibition of APH(3')-Ia by three diverse chemical scaffolds, anthrapyrazolone, 4-anilinoquinazoline and PP (pyrazolopyrimidine), and reveal distinctions in the binding mode of anthrapyrazolone and PP compounds to APH(3')-Ia compared with ePKs. Using this observation, we identify PP derivatives that select against ePKs, attenuate APH(3')-Ia activity and rescue aminoglycoside antibiotic activity against a resistant Escherichia coli strain. The structures described in the present paper and the inhibition studies provide an important opportunity for structure-based design of compounds to target aminoglycoside phosphotransferases for inhibition, potentially overcoming this form of antibiotic resistance.


    Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aminoglycoside 3'-phosphotransferase AphA1-IAB
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
272Acinetobacter baumannii AYEMutation(s): 0 
Gene Names: ABAYE3578APHA1-IAB
EC: 2.7.1.95
UniProt
Find proteins for B0VD92 (Acinetobacter baumannii (strain AYE))
Explore B0VD92 
Go to UniProtKB:  B0VD92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0VD92
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KAN
Query on KAN

Download Ideal Coordinates CCD File 
BB [auth G],
FC [auth L],
GA [auth D],
KB [auth H],
M [auth A],
BB [auth G],
FC [auth L],
GA [auth D],
KB [auth H],
M [auth A],
NA [auth E],
OB [auth I],
S [auth B],
TA [auth F],
VB [auth J],
Y [auth C],
ZB [auth K]
KANAMYCIN A
C18 H36 N4 O11
SBUJHOSQTJFQJX-NOAMYHISSA-N
 Ligand Interaction
0J9
Query on 0J9

Download Ideal Coordinates CCD File 
AA [auth C],
BC [auth K],
CB [auth G],
GC [auth L],
MB [auth H],
AA [auth C],
BC [auth K],
CB [auth G],
GC [auth L],
MB [auth H],
N [auth A],
OA [auth E],
PB [auth I],
T [auth B],
UA [auth F],
WB [auth J],
Z [auth C]
1-tert-butyl-3-(naphthalen-1-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C19 H19 N5
XSHQBIXMLULFEV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
IA [auth D],
LB [auth H],
MA [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AB [auth F],
AC [auth K],
DA [auth C],
DC [auth K],
EA [auth C],
AB [auth F],
AC [auth K],
DA [auth C],
DC [auth K],
EA [auth C],
EC [auth K],
FA [auth C],
FB [auth G],
GB [auth G],
HA [auth D],
HB [auth G],
IC [auth L],
JA [auth D],
JB [auth H],
JC [auth L],
KA [auth D],
KC [auth L],
LA [auth D],
LC [auth L],
MC [auth L],
NB [auth H],
P [auth A],
Q [auth A],
QA [auth E],
R [auth A],
RA [auth E],
SA [auth E],
SB [auth I],
TB [auth I],
UB [auth I],
W [auth B],
X [auth B],
XA [auth F],
XB [auth J],
YA [auth F],
ZA [auth F]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth C],
RB [auth I]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth C],
CC [auth K],
DB [auth G],
EB [auth G],
HC [auth L],
BA [auth C],
CC [auth K],
DB [auth G],
EB [auth G],
HC [auth L],
IB [auth H],
O [auth A],
PA [auth E],
QB [auth I],
U [auth B],
V [auth B],
VA [auth F],
WA [auth F],
YB [auth K]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
0J9 PDBBind:  4GKH Ki: 2.15e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: P 1
  • Diffraction Data DOI: 10.18430/M34GKH Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.185α = 102.97
b = 97.298β = 106.21
c = 112.738γ = 112.66
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references
  • Version 1.2: 2013-08-07
    Changes: Database references
  • Version 1.3: 2013-09-04
    Changes: Database references