6R4V

Crystal structure of human geranylgeranyl diphosphate synthase bound to ibandronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Metal Coordination Is Crucial for Geranylgeranyl Diphosphate Synthase-Bisphosphonate Interactions: A Crystallographic and Computational Analysis.

Lisnyansky, M.Yariv, E.Segal, O.Marom, M.Loewenstein, A.Ben-Tal, N.Giladi, M.Haitin, Y.

(2019) Mol Pharmacol 96: 580-588

  • DOI: 10.1124/mol.119.117499
  • Primary Citation of Related Structures:  
    6R4V

  • PubMed Abstract: 
  • Geranylgeranyl diphosphate synthase (GGPPS) is a central metalloenzyme in the mevalonate pathway, crucial for the prenylation of small GTPases. As small GTPases are pivotal for cellular survival, GGPPS was highlighted as a potential target for treating human diseases, including solid and hematologic malignancies and parasitic infections ...

    Geranylgeranyl diphosphate synthase (GGPPS) is a central metalloenzyme in the mevalonate pathway, crucial for the prenylation of small GTPases. As small GTPases are pivotal for cellular survival, GGPPS was highlighted as a potential target for treating human diseases, including solid and hematologic malignancies and parasitic infections. Most available GGPPS inhibitors are bisphosphonates, but the clinically available compounds demonstrate poor pharmacokinetic properties. Although the design of novel bisphosphonates with improved physicochemical properties is highly desirable, the structure of wild-type human GGPPS (hGGPPS) bound to a bisphosphonate has not been resolved. Moreover, various metal-bisphosphonate-binding stoichiometries were previously reported in structures of yeast GGPPS (yGGPPS), hampering computational drug design with metal-binding pharmacophores (MBP). In this study, we report the 2.2 Å crystal structure of hGGPPS in complex with ibandronate, clearly depicting the involvement of three Mg 2+ ions in bisphosphonate-protein interactions. Using drug-binding assays and computational docking, we show that the assignment of three Mg 2+ ions to the binding site of both hGGPPS and yGGPPS greatly improves the correlation between calculated binding energies and experimentally measured affinities. This work provides a structural basis for future rational design of additional MBP-harboring drugs targeting hGGPPS. SIGNIFICANCE STATEMENT: Bisphosphonates are inhibitors of geranylgeranyl diphosphate synthase (GGPPS), a metalloenzyme crucial for cell survival. Bisphosphonate binding depends on coordination by Mg 2+ ions, but various Mg 2+ -bisphosphonate-binding stoichiometries were previously reported. In this study, we show that three Mg 2+ ions are vital for drug binding and provide a structural basis for future computational design of GGPPS inhibitors.


    Organizational Affiliation

    Department of Physiology and Pharmacology, Sackler Faculty of Medicine (M.L., M.M., M.G., Y.H.), Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences (E.Y., N.B.-T.), and Sackler Faculty of Medicine (O.S., A.L.), Tel Aviv University, Tel Aviv, Israel; Ophthalmology Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel (A.L.); and Tel Aviv Sourasky Medical Center, Tel Aviv, Israel (M.G.) yhaitin@post.tau.ac.il.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Geranylgeranyl pyrophosphate synthaseA, E [auth B], B [auth C], F [auth D], D [auth E], C [auth F]307Homo sapiensMutation(s): 1 
Gene Names: GGPS1
EC: 2.5.1 (PDB Primary Data), 2.5.1.1 (PDB Primary Data), 2.5.1.29 (PDB Primary Data), 2.5.1.10 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O95749 (Homo sapiens)
Explore O95749 
Go to UniProtKB:  O95749
PHAROS:  O95749
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BFQ (Subject of Investigation/LOI)
Query on BFQ

Download Ideal Coordinates CCD File 
AA [auth B], EA [auth D], J [auth A], N [auth C], S [auth F], W [auth E]IBANDRONATE
C9 H23 N O7 P2
MPBVHIBUJCELCL-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth A], O [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth D] , CA [auth D] , DA [auth D] , G [auth A] , H [auth A] , I [auth A] , L [auth C] , M [auth C] , 
BA [auth D],  CA [auth D],  DA [auth D],  G [auth A],  H [auth A],  I [auth A],  L [auth C],  M [auth C],  P [auth F],  Q [auth F],  R [auth F],  T [auth E],  U [auth E],  V [auth E],  X [auth B],  Y [auth B],  Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BFQ Binding MOAD:  6R4V Kd: 1740 (nM) from 1 assay(s)
BindingDB:  6R4V IC50: min: 7.94e+4, max: 8.30e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.45α = 90
b = 153.01β = 90
c = 198.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael1775/12 and 1721/16
German Research FoundationGermanyI-2425-418.13/2016
Other privateIsraelShtacher Foundation
Other privateIsraelIsrael Cancer Research Foundation Grant 01214

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references