1BZY

HUMAN HGPRTASE WITH TRANSITION STATE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.249 (Depositor) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IMUClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

The 2.0 A structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with a transition-state analog inhibitor.

Shi, W.Li, C.M.Tyler, P.C.Furneaux, R.H.Grubmeyer, C.Schramm, V.L.Almo, S.C.

(1999) Nat Struct Biol 6: 588-593

  • DOI: https://doi.org/10.1038/9376
  • Primary Citation of Related Structures:  
    1BZY

  • PubMed Abstract: 

    The structure of human HGPRT bound to the transition-state analog immucillinGP and Mg2+-pyrophosphate has been determined to 2.0 A resolution. ImmucillinGP was designed as a stable analog with the stereoelectronic features of the transition state. Bound inhibitor at the catalytic site indicates that the oxocarbenium ion of the transition state is stabilized by neighboring-group participation from MgPPi and O5'. A short hydrogen bond forms between Asp 137 and the purine ring analog. Two Mg2+ ions sandwich the pyrophosphate and contact both hydroxyls of the ribosyl analog. The transition-state analog is shielded from bulk solvent by a catalytic loop that moves approximately 25 A to cover the active site and becomes an ordered antiparallel beta-sheet.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
A, B, C, D
217Homo sapiensMutation(s): 0 
EC: 2.4.2.8
UniProt & NIH Common Fund Data Resources
Find proteins for P00492 (Homo sapiens)
Explore P00492 
Go to UniProtKB:  P00492
PHAROS:  P00492
GTEx:  ENSG00000165704 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00492
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMU
Query on IMU

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C],
S [auth D]
PHOSPHORIC ACID MONO-[5-(2-AMINO-4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-3,4-DIHYDROXY-PYRROLIDIN-2-YLMETHYL] ESTER
C11 H16 N5 O7 P
IQLBECLICFDTTF-PVEDRDFWSA-N
POP
Query on POP

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
P [auth C],
T [auth D]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth B]
J [auth B]
M [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
IMU BindingDB:  1BZY Ki: min: 4.6, max: 56 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.249 (Depositor) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.96α = 90
b = 102.01β = 90
c = 144.27γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IMUClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-05-22
    Changes: Data collection