6BKW

BTK complex with compound 12

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1007/s10822-019-00187-y
  • Primary Citation of Related Structures:  
    6BIK, 6BKE, 6BKH, 6BKW, 6BLN, 6BQA, 6BQD, 6EP9

  • 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 displacement to achieve the largest gain in potency ...

    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: 

    Gilead Sciences Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase BTKA287Homo sapiensMutation(s): 0 
Gene Names: BTK, AGMX1, ATK, BPK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens)
Explore Q06187 
Go to UniProtKB:  Q06187
PHAROS:  Q06187
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06187
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DXM (Subject of Investigation/LOI)
Query on DXM
Download Ideal Coordinates CCD File 
E [auth A]N-(3-{5-[(1,5-dimethyl-1H-pyrazol-3-yl)amino]-1-methyl-6-oxo-1,6-dihydropyridazin-3-yl}-2,6-difluorophenyl)-4,5,6,7-tetrahydro-1-benzothiophene-2-carboxamide
C25 H24 F2 N6 O2 S
CAJCMVSBNVIKHV-UHFFFAOYSA-N		 Ligand Interaction
FPZ
Query on FPZ
Download Ideal Coordinates CCD File 
F [auth A]triphenylphosphane
C18 H15 P
RIOQSEWOXXDEQQ-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-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: 1.50 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.765α = 90
b = 108.765β = 90
c = 41.863γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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