6GIU

Human IMPase with L-690330


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Co-crystallization of human inositol monophosphatase with the lithium mimetic L-690,330.

Kraft, L.Roe, S.M.Gill, R.Atack, J.R.

(2018) Acta Crystallogr D Struct Biol 74: 973-978

  • DOI: 10.1107/S2059798318010380
  • Primary Citation of Related Structures:  
    6GIU, 6GJ0

  • PubMed Abstract: 
  • Lithium, which is still the gold standard in the treatment of bipolar disorder, has been proposed to inhibit inositol monophosphatase (IMPase) and is hypothesized to exert its therapeutic effects by attenuating phosphatidylinositol (PI) cell signalling. Drug-discovery efforts have focused on small-molecule lithium mimetics that would specifically inhibit IMPase without exhibiting the undesired side effects of lithium ...

    Lithium, which is still the gold standard in the treatment of bipolar disorder, has been proposed to inhibit inositol monophosphatase (IMPase) and is hypothesized to exert its therapeutic effects by attenuating phosphatidylinositol (PI) cell signalling. Drug-discovery efforts have focused on small-molecule lithium mimetics that would specifically inhibit IMPase without exhibiting the undesired side effects of lithium. L-690,330 is a potent bisphosphonate substrate-based inhibitor developed by Merck Sharp & Dohme. To aid future structure-based inhibitor design, determination of the exact binding mechanism of L-690,330 to IMPase was of interest. Here, the high-resolution X-ray structure of human IMPase in complex with L690,330 and manganese ions determined at 1.39 Å resolution is reported.


    Organizational Affiliation

    School of Biosciences, Medicines Discovery Institute, Park Place, Cardiff CF10 3AT, Wales.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inositol monophosphatase 1A, B277Homo sapiensMutation(s): 0 
Gene Names: IMPA1IMPA
EC: 3.1.3.25 (PDB Primary Data), 3.1.3.94 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P29218 (Homo sapiens)
Explore P29218 
Go to UniProtKB:  P29218
PHAROS:  P29218
GTEx:  ENSG00000133731 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29218
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L69 (Subject of Investigation/LOI)
Query on L69

Download Ideal Coordinates CCD File 
F [auth A],
W [auth B]
[1-(4-oxidanylphenoxy)-1-phosphono-ethyl]phosphonic acid
C8 H12 O8 P2
JKOCAAWWDVHWKB-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
G [auth A],
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
X [auth B],
Y [auth B],
Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
S [auth B],
T [auth B],
C [auth A],
D [auth A],
E [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
L69 BindingDB:  6GIU IC50: 330 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.29α = 90
b = 85.29β = 90
c = 151.51γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-05-15 
  • Released Date: 2018-10-17 
  • Deposition Author(s): Kraft, L.V., Roe, S.M.

Funding OrganizationLocationGrant Number
United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release