1RDT

Crystal Structure of a new rexinoid bound to the RXRalpha ligand binding doamin in the RXRalpha/PPARgamma heterodimer

Structural Biology Knowledgebase: 1RDT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.221

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1RDT

Classification: HORMONE / GROWTH FACTOR

Total Structure Weight: 65772.68

Macromolecule Entities
Molecule Chains Length Organism Details
Retinoic acid receptor RXR-alpha A 242 Homo sapiens Fragment: ligand binding doamin
Gene Name(s): RXRA Gene View NR2B1
LxxLL motif coactivator B 25 Homo sapiens EC#: 2.3.1.48 IUBMB
Fragment: LxxLL peptide
Gene Name(s): NCOA1 Gene View BHLHE74 SRC1
Peroxisome proliferator activated receptor gamma D 284 Homo sapiens Fragment: ligand binding doamin
Gene Name(s): PPARG Gene View NR1C3
LxxLL motif coactivator E 23 Homo sapiens EC#: 2.3.1.48 IUBMB
Fragment: LxxLL peptide
Gene Name(s): CREBBP Gene View CBP

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
570
Query on 570

D 2-(2-BENZOYL-PHENYLAMINO)-3-{4-[2-(5-METHYL- 2-PHENYL-OXAZOL-4-YL)-ETHOXY]-PHENYL}-PROPIONIC ACID
GI262570 (Synonym)
C34 H30 N2 O5
ZZCHHVUQYRMYLW-HKBQPEDESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
L79
Query on L79

A (S)-(2E)-3[4-(5,5,8,8-TETRAMETHYL-5,6,7,8- TETRAHYDRO-2-NAPHTHALENYL)TETRAHYDRO-1-BENZOFURAN- 2-YL]-2-PROPENOIC ACID
C25 H30 O3
WFLQBFXZEVUXMT-UEOKTHRPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
570 EC50: 0.339 - 6 nM (98 - 100) BindingDB
IC50: 25 - 217 nM (100) BindingDB
Ki: 1.1 nM (100) BindingDB

N/A in BindingMoad

L79 N/A in BindingDB
Ki: 6 nM  BindingMOAD
Ki: 200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.221
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 49.69 α = 90.00
b = 54.58 β = 90.00
c = 211.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-11-06
  • Released Date: 2004-11-09
  • Deposition author(s): Haffner, C.D., Lenhard, J.M., Miller, A.B., McDougald, D.L., Dwornik, K., Ittoop, O.R., Gampe Jr., R.T., Xu, H.E., Blanchard, S., Montana, V.G.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4