4IWV

Crystals structure of Human Glucokinase in complex with small molecule activator

PDB DOI: https://doi.org/10.2210/pdb4IWV/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.250
R-Value Work: 0.199
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 51.5 kDa
Atom Count: 3,687
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
1J9 Query on 1J9 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	(2S)-2-{[1-(2-chlorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]oxy}-N-(5-chloropyridin-2-yl)-3-(2-hydroxyethoxy)propanamide C₂₁ H₁₈ Cl₂ N₆ O₄ KTWRHJPPIZQGRW-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: 2.10 Å
R-Value Free: 0.250
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.938	α = 90
b = 77.938	β = 90
c = 85.35	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):

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
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary

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4IWV

Crystals structure of Human Glucokinase in complex with small molecule activator

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)