4PX5

Human GKRP bound to AMG-0696 and Sorbitol-6-phosphate

PDB DOI: https://doi.org/10.2210/pdb4PX5/pdb

Classification: sugar binding protein/inhibitor
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2014-03-21 Released: 2015-05-13
Deposition Author(s): Jordan, S.R., Chmait, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.279
R-Value Work: 0.220
R-Value Observed: 0.223

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., Cupple, R., Fotsch, C.

To be published.

Macromolecule Content

Total Structure Weight: 146.92 kDa
Atom Count: 9,380
Modelled Residue Count: 1,175
Deposited Residue Count: 1,276
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase regulatory protein	A, B	638	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14397
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2WZ Query on 2WZ Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain V [auth B] MOL2 format, chain C [auth A] MOL2 format, chain V [auth B] mmCIF format, chain C [auth A] mmCIF format, chain V [auth B]	C [auth A], V [auth B]	N-[(R)-(2-amino-5-chloro-3-fluoropyridin-4-yl){7-[4-(2-hydroxypropan-2-yl)pyridin-2-yl]-1-benzothiophen-2-yl}methyl]cyclopropanesulfonamide C₂₅ H₂₄ Cl F N₄ O₃ S₂ FBKAQPKUCXZNGQ-QFIPXVFZSA-N		Interactions Focus chain C [auth A] Focus chain V [auth B] Interactions & Density Focus chain C [auth A] Focus chain V [auth B]
S6P Query on S6P Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain W [auth B] MOL2 format, chain D [auth A] MOL2 format, chain W [auth B] mmCIF format, chain D [auth A] mmCIF format, chain W [auth B]	D [auth A], W [auth B]	D-SORBITOL-6-PHOSPHATE C₆ H₁₅ O₉ P GACTWZZMVMUKNG-SLPGGIOYSA-N		Interactions Focus chain D [auth A] Focus chain W [auth B] Interactions & Density Focus chain D [auth A] Focus chain W [auth B]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	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], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], X [auth B], Y [auth B], Z [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain U [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain U [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain U [auth A]	PA [auth B], QA [auth B], RA [auth B], SA [auth B], U [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain U [auth A] Interactions & Density Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain U [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain T [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain T [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain T [auth A]	NA [auth B], OA [auth B], T [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain NA [auth B] Focus chain OA [auth B] Focus chain T [auth A] Interactions & Density Focus chain NA [auth B] Focus chain OA [auth B] Focus chain T [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
2WZ	BindingDB: 4PX5	Kd: min: 1.2, max: 1.5 (nM) from 2 assay(s)
2WZ	BindingDB: 4PX5	IC50: 3.8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.279
R-Value Work: 0.220
R-Value Observed: 0.223
Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.453	α = 90
b = 148.453	β = 90
c = 132.283	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-05-13

Deposition Author(s):

Jordan, S.R.

Chmait, S.

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