6BKE

BTK complex with compound 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison.

Nittinger, E.Gibbons, P.Eigenbrot, C.Davies, D.R.Maurer, B.Yu, C.L.Kiefer, J.R.Kuglstatter, A.Murray, J.Ortwine, D.F.Tang, Y.Tsui, V.

(2019) J. Comput. Aided Mol. Des. 33: 307-330

  • DOI: 10.1007/s10822-019-00187-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Targeting the interaction with or displacement of the 'right' water molecule can significantly increase inhibitor potency in structure-guided drug design. Multiple computational approaches exist to predict which waters should be targeted for displace ...

    Targeting the interaction with or displacement of the 'right' water molecule can significantly increase inhibitor potency in structure-guided drug design. Multiple computational approaches exist to predict which waters should be targeted for displacement to achieve the largest gain in potency. However, the relative success of different methods remains underexplored. Here, we present a comparison of the ability of five water prediction programs (3D-RISM, SZMAP, WaterFLAP, WaterRank, and WaterMap) to predict crystallographic water locations, calculate their binding free energies, and to relate differences in these energies to observed changes in potency. The structural cohort included nine Bruton's Tyrosine Kinase (BTK) structures, and nine bromodomain structures. Each program accurately predicted the locations of most crystallographic water molecules. However, the predicted binding free energies correlated poorly with the observed changes in inhibitor potency when solvent atoms were displaced by chemical changes in closely related compounds.


    Organizational Affiliation

    Beryllium Discovery, 7869 NE Day Road West, Bainbridge Island, WA, 98110, USA.,F. Hoffman-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland.,Universit├Ąt Hamburg, ZBH - Center for Bioinformatics, Bundesstra├če 43, 20146, Hamburg, Germany. nittinger@zbh.uni-hamburg.de.,Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA. gibbons.paul@gene.com.,Relay Therapeutics, 215 First Street, 3rd Floor, Cambridge, MA, 02142, USA.,Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA. charleseigenbrot@comcast.net.,Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Constellation Pharmaceuticals, 215 First Street, Cambridge, MA, 02142, USA.,Gilead Sciences Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase BTK
A
287Homo sapiensMutation(s): 0 
Gene Names: BTK (AGMX1, ATK, BPK)
EC: 2.7.10.2
Find proteins for Q06187 (Homo sapiens)
Go to Gene View: BTK
Go to UniProtKB:  Q06187
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DVJ
Query on DVJ

Download SDF File 
Download CCD File 
A
N-[2-(2-hydroxyethyl)-3-{5-[(5-methyl-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazin-2-yl)amino]-6-oxo-1,6-dihydropyridazin-3-yl}phenyl]-1-benzothiophene-2-carboxamide
C28 H27 N7 O3 S
MFRXRCVCUQSDMP-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.188 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 108.198α = 90.00
b = 108.198β = 90.00
c = 41.942γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-02-27
    Type: Data collection, Database references
  • Version 1.2: 2019-03-27
    Type: Data collection, Database references