6DMI

A multiconformer ligand model of 5T5 bound to BACE-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 5EZX - determined by Banner, D., Benz, J., Stihle, M., Kuglstatter, A.  

Literature

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps.

van Zundert, G.Hudson, B.M.de Oliveira, S.Keedy, D.A.Fonseca, R.Heliou, A.Suresh, P.Borrelli, K.Day, T.Fraser, J.van den Bedem, H.

(2018) J. Med. Chem. --: --

  • DOI: 10.1021/acs.jmedchem.8b01292
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and ent ...

    Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. In an analysis of the cancer related BRD4 domain, we found that up to 29% of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively iso-energetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multi-temperature crystallography could therefore augment the structure-based drug design toolbox.


    Related Citations: 
    • A Real-World Perspective on Molecular Design.
      Kuhn, B.,Guba, W.,Hert, J.,Banner, D.,Bissantz, C.,Ceccarelli, S.,Haap, W.,Korner, M.,Kuglstatter, A.,Lerner, C.,Mattei, P.,Neidhart, W.,Pinard, E.,Rudolph, M.G.,Schulz-Gasch, T.,Woltering, T.,Stahl, M.
      (2016) J. Med. Chem. 59: 4087



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
390Homo sapiensMutation(s): 0 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5T5
Query on 5T5

Download SDF File 
Download CCD File 
A
[(1~{R},2~{R})-2-[(4~{S})-2-azanyl-4-[4-[bis(fluoranyl)methoxy]phenyl]-5~{H}-1,3-oxazol-4-yl]cyclopropyl]-(5-chloranylpyridin-3-yl)methanone
C19 H16 Cl F2 N3 O3
AVRZQFKBYKMVDH-SPYBWZPUSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.320α = 90.00
b = 102.320β = 90.00
c = 169.820γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release