4MQU | pdb_00004mqu

Human GKRP complexed to AMG-3969 and S6P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 
    0.277 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 4MQU

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Small molecule disruptors of the glucokinase-glucokinase regulatory protein interaction: 2. Leveraging structure-based drug design to identify analogues with improved pharmacokinetic profiles.

St Jean, D.J.Ashton, K.S.Bartberger, M.D.Chen, J.Chmait, S.Cupples, R.Galbreath, E.Helmering, J.Hong, F.T.Jordan, S.R.Liu, L.Kunz, R.K.Michelsen, K.Nishimura, N.Pennington, L.D.Poon, S.F.Reid, D.Sivits, G.Stec, M.M.Tadesse, S.Tamayo, N.Van, G.Yang, K.C.Zhang, J.Norman, M.H.Fotsch, C.Lloyd, D.J.Hale, C.

(2014) J Med Chem 57: 325-338

  • DOI: https://doi.org/10.1021/jm4016747
  • Primary Citation Related Structures: 
    4MQU, 4MRO

  • PubMed Abstract: 

    In the previous report , we described the discovery and optimization of novel small molecule disruptors of the GK-GKRP interaction culminating in the identification of 1 (AMG-1694). Although this analogue possessed excellent in vitro potency and was a useful tool compound in initial proof-of-concept experiments, high metabolic turnover limited its advancement. Guided by a combination of metabolite identification and structure-based design, we have successfully discovered a potent and metabolically stable GK-GKRP disruptor (27, AMG-3969). When administered to db/db mice, this compound demonstrated a robust pharmacodynamic response (GK translocation) as well as statistically significant dose-dependent reductions in fed blood glucose levels.


  • Organizational Affiliation
    • Department of Therapeutic Discovery-Medicinal Chemistry, ‡Department of Therapeutic Discovery-Molecular Structure and Characterization, §Department of Metabolic Disorders, ∥Department of Pharmacokinetics and Drug Metabolism, ⊥Department of Pathology, #Department of Pharmaceutics Amgen, Inc. , One Amgen Center Drive, Thousand Oaks, California, 91320 and 360 Binney Street, Cambridge, Massachusetts, 02142, United States.

Macromolecule Content 

  • Total Structure Weight: 145.48 kDa 
  • Atom Count: 9,456 
  • Modeled Residue Count: 1,175 
  • Deposited Residue Count: 1,272 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glucokinase regulatory protein
A, B
636Homo 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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG9

Query on MG9



Download:Ideal Coordinates CCD File
C [auth A],
Q [auth B]
2-{4-[(2S)-4-[(6-aminopyridin-3-yl)sulfonyl]-2-(prop-1-yn-1-yl)piperazin-1-yl]phenyl}-1,1,1,3,3,3-hexafluoropropan-2-ol
C21 H20 F6 N4 O3 S
SIFKNECWLVONIH-INIZCTEOSA-N
S6P

Query on S6P



Download:Ideal Coordinates CCD File
D [auth A],
R [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],
G [auth A],
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],
S [auth B],
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
GA [auth B],
HA [auth B],
IA [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
FA [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MG9 BindingDB:  4MQU IC50: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free:  0.277 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.066α = 90
b = 149.066β = 90
c = 132.463γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
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: 2014-05-07
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2024-04-03
    Changes: Refinement description