2XP8

DISCOVERY OF CELL-ACTIVE PHENYL-IMIDAZOLE PIN1 INHIBITORS BY STRUCTURE-GUIDED FRAGMENT EVOLUTION

Structural Biology Knowledgebase: 2XP8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.315
  • R-Value Work: 0.265

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2XP8

Classification: ISOMERASE

Total Structure Weight: 19372.65

Macromolecule Entities
Molecule Chains Length Organism Details
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1 A 167 Homo sapiens EC#: 5.2.1.8 IUBMB
Mutation: R14A
Gene Name(s): PIN1 Gene View

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
12P
Query on 12P

A DODECAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400 (Synonym)
C24 H50 O13
WRZXKWFJEFFURH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
4FY
Query on 4FY

A 4-(MORPHOLIN-4-YLCARBONYL)-2-PHENYL-1H-IMIDAZOLE- 5-CARBOXYLIC ACID
C15 H15 N3 O4
VLPLWGMKNLKROX-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
4FY IC50: 15000 nM (99) BindingDB

Kd: 15000 nM  BindingMOAD
IC50: 15000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.315
  • R-Value Work: 0.265
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.03 α = 90.00
b = 68.03 β = 90.00
c = 79.29 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-08-25
  • Released Date: 2011-01-12
  • Deposition author(s): Potter, A., Oldfield, V., Nunns, C., Fromont, C., Ray, S., Northfield, C.J., Bryant, C.J., Scrace, S.F., Robinson, D., Matossova, N., Baker, L., Dokurno, P., Surgenor, A.E., Davis, B.E., Richardson, C.M., Murray, J.B., Moore, J.D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4