5U5U

CcP gateless cavity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/10.1073/pnas.1703287114
  • Primary Citation of Related Structures:  
    5U5U, 5U5V, 5U5W, 5U5X, 5U5Y, 5U5Z, 5U60, 5U61, 5UG2

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxidase289Saccharomyces cerevisiae RM11-1aMutation(s): 2 
Gene Names: SCRG_04081
EC: 1.11.1
UniProt
Find proteins for B3LRE1 (Saccharomyces cerevisiae (strain RM11-1a))
Explore B3LRE1 
Go to UniProtKB:  B3LRE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3LRE1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NTN
Query on NTN

Download Ideal Coordinates CCD File 
C [auth A]ISONICOTINAMIDINE
C6 H7 N3
BIJRUEBMNUUNIJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NTN Binding MOAD:  5U5U Kd: 6.19e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.007α = 90
b = 74.92β = 90
c = 106.941γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM59957 OD009180 GM110580

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Database references
  • Version 1.4: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.6: 2024-03-06
    Changes: Data collection, Database references