5EMS

Crystal Structure of an iodinated insulin analog

  • Classification: HORMONE
  • Organism(s): Homo sapiens
  • Mutation(s): 

  • Deposited: 2015-11-06 Released: 2016-11-16 
  • Deposition Author(s): Lawrence, M.C., Pandyarajan, V., Wan, Z., Weiss, M.A.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease; National Institutes of Health/National Institute of General Medical Sciences; National Health and Medical Research Council (Australia) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Extending Halogen-based Medicinal Chemistry to Proteins: IODO-INSULIN AS A CASE STUDY.

El Hage, K.Pandyarajan, V.Phillips, N.B.Smith, B.J.Menting, J.G.Whittaker, J.Lawrence, M.C.Meuwly, M.Weiss, M.A.

(2016) J. Biol. Chem. 291: 27023-27041

  • DOI: 10.1074/jbc.M116.761015

  • PubMed Abstract: 
  • Insulin, a protein critical for metabolic homeostasis, provides a classical model for protein design with application to human health. Recent efforts to improve its pharmaceutical formulation demonstrated that iodination of a conserved tyrosine (TyrB ...

    Insulin, a protein critical for metabolic homeostasis, provides a classical model for protein design with application to human health. Recent efforts to improve its pharmaceutical formulation demonstrated that iodination of a conserved tyrosine (TyrB26) enhances key properties of a rapid-acting clinical analog. Moreover, the broad utility of halogens in medicinal chemistry has motivated the use of hybrid quantum- and molecular-mechanical methods to study proteins. Here, we (i) undertook quantitative atomistic simulations of 3-[iodo-TyrB26]insulin to predict its structural features, and (ii) tested these predictions by X-ray crystallography. Using an electrostatic model of the modified aromatic ring based on quantum chemistry, the calculations suggested that the analog, as a dimer and hexamer, exhibits subtle differences in aromatic-aromatic interactions at the dimer interface. Aromatic rings (TyrB16, PheB24, PheB25, 3-I-TyrB26, and their symmetry-related mates) at this interface adjust to enable packing of the hydrophobic iodine atoms within the core of each monomer. Strikingly, these features were observed in the crystal structure of a 3-[iodo-TyrB26]insulin analog (determined as an R6 zinc hexamer). Given that residues B24-B30 detach from the core on receptor binding, the environment of 3-I-TyrB26 in a receptor complex must differ from that in the free hormone. Based on the recent structure of a "micro-receptor" complex, we predict that 3-I-TyrB26 engages the receptor via directional halogen bonding and halogen-directed hydrogen bonding as follows: favorable electrostatic interactions exploiting, respectively, the halogen's electron-deficient σ-hole and electronegative equatorial band. Inspired by quantum chemistry and molecular dynamics, such "halogen engineering" promises to extend principles of medicinal chemistry to proteins.


    Organizational Affiliation

    From the Department of Chemistry, University of Basel, Klingelbergstrasse 80 CH-4056 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin
A, C, E, G, I, K
21Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Insulin
B, D, F, H, J, L
30Homo sapiensMutation(s): 1 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
D, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
IPH
Query on IPH

Download SDF File 
Download CCD File 
A, C, E, G, I, K
PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
IYR
Query on IYR
B, D, F, H, J, L
L-PEPTIDE LINKINGC9 H10 I N O3TYR
NLE
Query on NLE
B, D, F, H, J, L
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.430α = 90.00
b = 61.630β = 111.38
c = 58.580γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

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 Diabetes and Digestive and Kidney DiseaseUnited StatesR01 DK04949
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK079233
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesF30 DK094685-04
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM007250
National Health and Medical Research Council (Australia)Australia1005896
National Health and Medical Research Council (Australia)Australia1058233
National Health and Medical Research Council (Australia)Australia361646

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-11-23
    Type: Database references
  • Version 1.2: 2016-12-21
    Type: Database references
  • Version 1.3: 2017-01-11
    Type: Database references
  • Version 1.4: 2017-09-27
    Type: Author supporting evidence