4PX3 | pdb_00004px3

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

PDB DOI: https://doi.org/10.2210/pdb4PX3/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: 2.43 Å
R-Value Free:
0.258 (Depositor), 0.259 (DCC)
R-Value Work:
0.196 (Depositor), 0.201 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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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.

Macromolecule Content

Total Structure Weight: 146.11 kDa
Atom Count: 9,324
Modeled Residue Count: 1,175
Deposited Residue Count: 1,276
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14397
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2WX Query on 2WX Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain C [auth A] MOL2 format, chain R [auth B] MOL2 format, chain C [auth A] mmCIF format, chain R [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain R [auth B]
S6P Query on S6P Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain D [auth A] MOL2 format, chain S [auth B] MOL2 format, chain D [auth A] mmCIF format, chain S [auth B] mmCIF format, chain D [auth A]	D [auth A], S [auth B]	D-SORBITOL-6-PHOSPHATE C₆ H₁₅ O₉ P GACTWZZMVMUKNG-SLPGGIOYSA-N		Interactions Focus chain D [auth A] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain S [auth B]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [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], 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		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 I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] 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 I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] 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 IA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain JA [auth B]	IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain HA [auth B]	HA [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Interactions & Density Focus chain HA [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
2WX	BindingDB: 4PX3	Kd: 19 (nM) from 1 assay(s)
2WX	BindingDB: 4PX3	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 (Depositor), 0.259 (DCC)
R-Value Work: 0.196 (Depositor), 0.201 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.873	α = 90
b = 148.873	β = 90
c = 132.326	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

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Ligand Structure Quality Assessment

View more in-depth experimental data

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