5U5Z

CcP gateless cavity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Testing inhomogeneous solvation theory in structure-based ligand discovery.

Balius, T.E.Fischer, M.Stein, R.M.Adler, T.B.Nguyen, C.N.Cruz, A.Gilson, M.K.Kurtzman, T.Shoichet, B.K.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E6839-E6846

  • DOI: 10.1073/pnas.1703287114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Binding-site water is often displaced upon ligand recognition, but is commonly neglected in structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become popular for treating this effect, but it has not been tested in controlled e ...

    Binding-site water is often displaced upon ligand recognition, but is commonly neglected in structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become popular for treating this effect, but it has not been tested in controlled experiments at atomic resolution. To do so, we turned to a grid-based version of this method, GIST, readily implemented in molecular docking. Whereas the term only improves docking modestly in retrospective ligand enrichment, it could be added without disrupting performance. We thus turned to prospective docking of large libraries to investigate GIST's impact on ligand discovery, geometry, and water structure in a model cavity site well-suited to exploring these terms. Although top-ranked docked molecules with and without the GIST term often overlapped, many ligands were meaningfully prioritized or deprioritized; some of these were selected for testing. Experimentally, 13/14 molecules prioritized by GIST did bind, whereas none of the molecules that it deprioritized were observed to bind. Nine crystal complexes were determined. In six, the ligand geometry corresponded to that predicted by GIST, for one of these the pose without the GIST term was wrong, and three crystallographic poses differed from both predictions. Notably, in one structure, an ordered water molecule with a high GIST displacement penalty was observed to stay in place. Inclusion of this water-displacement term can substantially improve the hit rates and ligand geometries from docking screens, although the magnitude of its effects can be small and its impact in drug binding sites merits further controlled studies.


    Related Citations: 
    • Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.
      Fischer, M.,Coleman, R.G.,Fraser, J.S.,Shoichet, B.K.
      (2014) Nat Chem 6: 575


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxidase
A
289Saccharomyces cerevisiae (strain RM11-1a)Mutation(s): 2 
EC: 1.11.1.-
Find proteins for B3LRE1 (Saccharomyces cerevisiae (strain RM11-1a))
Go to UniProtKB:  B3LRE1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7VP
Query on 7VP

Download SDF File 
Download CCD File 
A
4-methyl-2-phenyl-1H-imidazole
C10 H10 N2
TYOXIFXYEIILLY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7VPKd: 3472000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.251α = 90.00
b = 73.239β = 90.00
c = 104.829γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM59957 OD009180 GM110580

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Database references
  • Version 1.4: 2017-09-20
    Type: Author supporting evidence