3V3V

Structural and functional analysis of quercetagetin, a natural JNK1 inhibitor

Structural Biology Knowledgebase: 3V3V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.227

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3V3V

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 46038.56

Macromolecule Entities
Molecule Chains Length Organism Details
Mitogen-activated protein kinase 8 A 379 Homo sapiens EC#: 2.7.11.24 IUBMB
Fragment: UNP residues 1-363
Mutation: Y185E, K288A, E364P, E365K
Gene Name(s): MAPK8 Gene View JNK1 PRKM8 SAPK1 SAPK1C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
C-Jun-amino-terminal kinase-interacting protein 1 B 11 Mus musculus Fragment: UNP residues 153-163
Gene Name(s): Mapk8ip1 Ib1 Jip1 Mapk8ip Prkm8ip
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 3,5,6,7-TETRAHYDROXY-2-(3,4-DIHYDROXYPHENYL)- 4H-CHROMEN-4-ONE
5, (Synonym)
C15 H10 O8
ZVOLCUVKHLEPEV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MYU N/A in BindingDB
N/A in BindingMoad
IC50: 4600 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.227
  • Space Group: I 4 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 172.37 α = 90.00
b = 172.37 β = 90.00
c = 86.04 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-14
  • Released Date: 2012-12-05
  • Deposition author(s): Baek, S., Kang, N.J., Popowicz, G.M., Arciniega, M., Jung, S.K., Byun, S., Song, N.R., Heo, Y.S., Kim, B.Y., Lee, H.J., Holak, T.A., Augustin, M., Bode, A.M., Huber, R., Dong, Z., Lee, K.W.

Revision History

  • 2013-01-30
    Type: Citation | Details: Citation update