3KAG

Structure-guided design of alpha-amino acid-derived Pin1 inhibitors

Structural Biology Knowledgebase: 3KAG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.202

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3KAG

Classification: ISOMERASE

Total Structure Weight: 19384.62

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)
4D7
Query on 4D7

A 3-(1H-benzimidazol-2-yl)-N-[(2-methylfuran- 3-yl)carbonyl]-D-alanine
(R)-3-(1H-Benzoimidazol-2-yl)-2-[(2-methyl- furan-3-carbonyl)-amino]-propionic acid (Synonym)
C16 H15 N3 O4
IBXZTXVMQARJHH-CYBMUJFWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
4D7 IC50: 6600 nM (99) BindingDB

IC50: 6600 nM  BindingMOAD
IC50: 6600 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.202
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.50 α = 90.00
b = 68.50 β = 90.00
c = 79.56 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-19
  • Released Date: 2009-12-22
  • Deposition author(s): Baker, L.M., Dokurno, P., Robinson, D.A., Surgenor, A.E., Murray, J.B., Potter, A.J., Moore, J.D.

Revision History

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