4OLH

Human GKRP Bound to AMG5106 and Sorbitol-6-Phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Small molecule disruptors of the glucokinase-glucokinase regulatory protein interaction: 4. Exploration of a novel binding pocket.

Hong, F.T.Norman, M.H.Ashton, K.S.Bartberger, M.D.Chen, J.Chmait, S.Cupples, R.Fotsch, C.Jordan, S.R.Lloyd, D.J.Sivits, G.Tadesse, S.Hale, C.St Jean, D.J.

(2014) J Med Chem 57: 5949-5964

  • DOI: https://doi.org/10.1021/jm5001979
  • Primary Citation of Related Structures:  
    4OLH

  • PubMed Abstract: 

    Structure-activity relationship investigations conducted at the 5-position of the N-pyridine ring of a series of N-arylsulfonyl-N'-2-pyridinyl-piperazines led to the identification of a novel bis-pyridinyl piperazine sulfonamide (51) that was a potent disruptor of the glucokinase-glucokinase regulatory protein (GK-GKRP) interaction. Analysis of the X-ray cocrystal of compound 51 bound to hGKRP revealed that the 3-pyridine ring moiety occupied a previously unexplored binding pocket within the protein. Key features of this new binding mode included forming favorable contacts with the top face of the Ala27-Val28-Pro29 ("shelf region") as well as an edge-to-face interaction with the Tyr24 side chain. Compound 51 was potent in both biochemical and cellular assays (IC50=0.005 μM and EC50=0.205 μM, respectively) and exhibited acceptable pharmacokinetic properties for in vivo evaluation. When administered to db/db mice (100 mg/kg, po), compound 51 demonstrated a robust pharmacodynamic effect and significantly reduced blood glucose levels up to 6 h postdose.


  • Organizational Affiliation

    Departments of Therapeutic Discovery-Medicinal Chemistry, ‡ Therapeutic Discovery-Molecular Structure, §Pharmacokinetics and Drug Metabolism, and ∥Metabolic Disorders, Amgen, Inc. , One Amgen Center Drive, Thousand Oaks, California 91320-1799, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucokinase Regulatory Protein
A, B
638Homo sapiensMutation(s): 0 
Gene Names: GCKR
UniProt & NIH Common Fund Data Resources
Find proteins for Q14397 (Homo sapiens)
Explore Q14397 
Go to UniProtKB:  Q14397
PHAROS:  Q14397
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14397
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2TO
Query on 2TO

Download Ideal Coordinates CCD File 
C [auth A],
R [auth B]
2-(2-{4-[(6-aminopyridin-3-yl)sulfonyl]piperazin-1-yl}-3,3'-bipyridin-5-yl)-1,1,1,3,3,3-hexafluoropropan-2-ol
C22 H20 F6 N6 O3 S
WSCXEOSPTMGMGQ-UHFFFAOYSA-N
S6P
Query on S6P

Download Ideal Coordinates CCD File 
D [auth A],
S [auth B]
D-SORBITOL-6-PHOSPHATE
C6 H15 O9 P
GACTWZZMVMUKNG-SLPGGIOYSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
E [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4
Query on SO4

Download Ideal Coordinates CCD File 
IA [auth B],
JA [auth B],
KA [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
HA [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.344α = 90
b = 149.344β = 90
c = 133.138γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2014-10-08
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary