2PFH

Complex of Aldose Reductase with NADP+ and simaltaneously bound competetive inhibitors Fidarestat and IDD594. Concentration of Fidarestat in soaking solution is less than concentration of IDD594.

Structural Biology Knowledgebase: 2PFH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.095
  • R-Value Work: 0.082

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2PFH

Classification: OXIDOREDUCTASE

Total Structure Weight: 37759.25

Macromolecule Entities
Molecule Chains Length Organism Details
Aldose reductase A 316 Homo sapiens EC#: 1.1.1.21 IUBMB
Mutation: L4I
Gene Name(s): AKR1B1 Gene View ALDR1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDP
Query on NDP

A NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LDT
Query on LDT

A IDD594
[2-(4-BROMO-2-FLUORO-BENZYLTHIOCARBAMOYL)- 5-FLUORO-PHENOXY]-ACETIC ACID (Synonym)
C16 H12 Br F2 N O3 S
JCZUIWYXULSXSW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FID
Query on FID

A (2S,4S)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN- 4,4'-IMIDAZOLIDINE]-2',5'-DIONE
FIDARESTAT (Synonym)
C12 H10 F N3 O4
WAAPEIZFCHNLKK-UFBFGSQYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CIT
Query on CIT

A CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LDT IC50: 30 nM (99) BindingDB
ΔG: -40.9 - -31.3 kJ/mol (99) BindingDB
-TΔS: -22.6 - 8 kJ/mol (99) BindingDB

Kd: 61 nM  BindingMOAD
N/A in PDBbind
FID IC50: 9 - 35 nM (85 - 99) BindingDB
ΔG: -46.7 - -35.4 kJ/mol (99) BindingDB
-TΔS: -9.8 - 29.7 kJ/mol (99) BindingDB

Kd: 6.5 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.095
  • R-Value Work: 0.082
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 49.15 α = 90.00
b = 66.55 β = 92.31
c = 47.24 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-04-05
  • Released Date: 2007-04-17
  • Deposition author(s): Petrova, T., Hazemann, I., Cousido, A., Mitschler, A., Ginell, S., Joachimiak, A., Podjarny, A.

Revision History

  • 2012-10-17
    Type: Citation | Details: Citation update
  • 2012-07-25
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4