4HVS

Crystal structure of KIT kinase domain with a small molecule inhibitor, PLX647

Structural Biology Knowledgebase: 4HVS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HVS

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 38424.80

Macromolecule Entities
Molecule Chains Length Organism Details
Mast/stem cell growth factor receptor Kit A 335 Homo sapiens EC#: 2.7.10.1 IUBMB
Fragment: KIT kinase domain with KID deleted
Mutation: I563S, V569S, Y609Q, L631S, M651E, I662H, I690H, C691S, K693D, Q694T, E753S, ΔD696, ΔH697, ΔA698, ΔE699, ΔA700, ΔA701, ΔL702, ΔY703, ΔK704, ΔN705, ΔL706, ΔL707, ΔK710, ΔE711, ΔS712, ΔS713, ΔC714, ΔS717, ΔT718, ΔN719, ΔE720, ΔY721, ΔM722, ΔD723, ΔM724, ΔK725, ΔP726, ΔG727, ΔV728, ΔS729, ΔY730, ΔV731, ΔV732, ΔP733, ΔK735, ΔA736, ΔD737, ΔK738, ΔR739, ΔR740, ΔS741, ΔV742, ΔR743, ΔI744, ΔG745, ΔY747, ΔI748, ΔE749, ΔR750, ΔD751, ΔV752, ΔT753, I756S, L762N, V825D, C844S, L890S, L912D, L923D
Gene Name(s): KIT Gene View SCFR
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
647
Query on 647

A 5-(1H-pyrrolo[2,3-b]pyridin-3-ylmethyl)-N- [4-(trifluoromethyl)benzyl]pyridin-2-amine
C21 H17 F3 N4
NODCQQSEMCESEC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
647 N/A in BindingDB
IC50: 16 nM  BindingMOAD
IC50: 16 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.199
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 110.74 α = 90.00
b = 81.86 β = 107.81
c = 50.06 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-06
  • Released Date: 2013-03-27
  • Deposition author(s): Zhang, Y., Zhang, C.

Revision History

  • 2013-04-17
    Type: Citation | Details: Citation update