4PX3

Human GKRP bound to AMG-3295 and Sorbitol-6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Structure-Guided Optimization of Diarylmethanesulfonamide Disruptors of GK-GKRP Binding

Pennington, L.D.Bartberger, M.D.Croghan, M.D.Andrews, K.L.Ashton, K.S.Bourbeau, M.P.Chen, J.Chmait, S.Cupples, R.Fotsch, C.

To be published.

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
2WX
Query on 2WX

Download Ideal Coordinates CCD File 
C [auth A],
R [auth B]
N-[(R)-1-benzothiophen-2-yl(2-chlorophenyl)methyl]-3,4-dihydro-2H-1,5-benzodioxepine-7-sulfonamide
C24 H20 Cl N O4 S2
TYGYAUYMFQMBTE-XMMPIXPASA-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],
LA [auth B],
MA [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
Binding Affinity Annotations 
IDSourceBinding Affinity
2WX BindingDB:  4PX3 Kd: 19 (nM) from 1 assay(s)
IC50: 17 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.873α = 90
b = 148.873β = 90
c = 132.326γ = 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: 2015-05-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary