4IXC

Crystal structure of Human Glucokinase in complex with a small molecule activator.

PDB DOI: https://doi.org/10.2210/pdb4IXC/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-01-25 Released: 2013-04-24
Deposition Author(s): Ogg, D.J., Hargreaves, D., Gerhardt, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.249
R-Value Work: 0.186
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Matched triplicate design sets in the optimisation of glucokinase activators maximising medicinal chemistry information content

Waring, M.J., Bennett, S.N.L., Boyd, S., Campbell, L., Davies, R.D.M., Gerhardt, S., Hargreaves, D., G Martin, N., Robb, G.R., Wilkinson, G.

To be published.

Macromolecule Content

Total Structure Weight: 51.48 kDa
Atom Count: 3,755
Modelled Residue Count: 443
Deposited Residue Count: 456
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 isoform 3	A	456	Homo sapiens	Mutation(s): 4 Gene Names: GCK EC: 2.7.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for P35557 (Homo sapiens) Explore P35557 Go to UniProtKB: P35557
PHAROS: P35557 GTEx: ENSG00000106633
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35557
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1JD Query on 1JD Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	(2S)-2-{[1-(3-chloropyridin-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]oxy}-N-(5-methylpyridin-2-yl)-3-(propan-2-yloxy)propanamide C₂₂ H₂₂ Cl N₇ O₃ AAGISEXHOPCAHZ-KRWDZBQOSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.249
R-Value Work: 0.186
R-Value Observed: 0.190
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.628	α = 90
b = 77.628	β = 90
c = 85.824	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-04-24

Deposition Author(s):

Ogg, D.J.

Hargreaves, D.

Gerhardt, S.

Revision History (Full details and data files)

Version 1.0: 2013-04-24
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

4IXC

Crystal structure of Human Glucokinase in complex with a small molecule activator.

Matched triplicate design sets in the optimisation of glucokinase activators maximising medicinal chemistry information content

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)