4L5B

Human dCK C4S-S74E mutant in complex with UDP and the DI-43 inhibitor

Structural Biology Knowledgebase: 4L5B SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.188

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4L5B

Classification: transferase / transferase inhibitor

Total Structure Weight: 67163.47

Macromolecule Entities
Molecule Chains Length Organism Details
Deoxycytidine kinase A, B 280 Homo sapiens EC#: 2.7.1.74 IUBMB
Fragment: Human deoxycytidine kinase
Mutation: C9S, C45S, C59S, S74E, C146S
Gene Name(s): DCK Gene View

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1UX
Query on 1UX

A, B 1-[5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}- 5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]- 2-methylpropan-2-ol
C22 H29 N5 O3 S2
PWASXBOUTAWHOZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UDP
Query on UDP

A, B URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1UX IC50: 1.4 - 15 nM (98) BindingDB
Ki: 0.8 nM (98) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.188
  • Space Group: P 41

Unit Cell:

Length (Å) Angle (°)
a = 68.67 α = 90.00
b = 68.67 β = 90.00
c = 120.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-06-10
  • Released Date: 2013-09-18
  • Deposition author(s): Nomme, J., Lavie, A.

Revision History

  • 2013-11-27
    Type: Citation | Details: Citation update