6TX6

CRYSTAL STRUCTURE OF HUMAN FKBP51 FK1 DOMAIN A19T MUTANT IN COMPLEX WITH NICOTINAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.111 
  • R-Value Observed: 0.111 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Hybrid Screening Approach for Very Small Fragments: X-ray and Computational Screening on FKBP51.

Draxler, S.W.Bauer, M.Eickmeier, C.Nadal, S.Nar, H.Rangel Rojas, D.Seeliger, D.Zeeb, M.Fiegen, D.

(2020) J Med Chem 63: 5856-5864

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00120
  • Primary Citation of Related Structures:  
    6TX4, 6TX5, 6TX6, 6TX7, 6TX8, 6TX9, 6TXX

  • PubMed Abstract: 

    Fragment-based drug discovery (FBDD) permits efficient sampling of the vast chemical space for hit identification. Libraries are screened biophysically and fragment:protein co-structures are determined by X-ray crystallography. In parallel, computational methods can derive pharmacophore models or screen virtual libraries. We screened 15 very small fragments (VSFs) (HA ≤ 11) computationally, using site identification by ligand competitive saturation (SILCS), and experimentally, by X-ray crystallography, to map potential interaction sites on the FKBP51 FK1 domain. We identified three hot spots and obtained 6 X-ray co-structures, giving a hit rate of 40%. SILCS FragMaps overlapped with X-ray structures. The compounds had millimolar affinities as determined by 15 N HSQC NMR. VSFs identified the same interactions as known FK1 binder and provide new chemical starting points. We propose a hybrid screening strategy starting with SILCS, followed by a pharmacophore-derived X-ray screen and 15 N HSQC NMR based KD determination to rapidly identify hits and their binding poses.


  • Organizational Affiliation

    Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstraße 65, 88397 Biberach, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP5128Homo sapiensMutation(s): 1 
Gene Names: FKBP5AIG6FKBP51
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q13451 (Homo sapiens)
Explore Q13451 
Go to UniProtKB:  Q13451
PHAROS:  Q13451
GTEx:  ENSG00000096060 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13451
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.111 
  • R-Value Observed: 0.111 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.407α = 90
b = 54.372β = 90
c = 56.738γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2020-06-24
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description