4GPT

Crystal structure of KPT251 in complex with CRM1-Ran-RanBP1

Structural Biology Knowledgebase: 4GPT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.165

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GPT

Classification: PROTEIN TRANSPORT / INHIBITOR

Total Structure Weight: 163639.91

Macromolecule Entities
Molecule Chains Length Organism Details
GTP-binding nuclear protein Ran A 216 Homo sapiens Gene Name(s): RAN Gene View ARA24 OK/SW-cl.81
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ran-specific GTPase-activating protein 1 B 140 Saccharomyces cerevisiae Fragment: UNP residues 62-201
Mutation: M79A, A98K
Gene Name(s): YRB1 CST20 HTN1 Gene View SFO1 YDR002W YD8119.08
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Exportin-1 C 1060 Saccharomyces cerevisiae Fragment: UNP residues 1-1058
Mutation: T539C, Y1022C
Gene Name(s): CRM1 KAP124 XPO1 Gene View YGR218W G8514
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GNP
Query on GNP

A PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
51K
Query on 51K

C 2-(2-{3-[3,5-bis(trifluoromethyl)phenyl]- 1H-1,2,4-triazol-1-yl}ethyl)-1,3,4-oxadiazole
KPT-251 (Synonym)
C14 H9 F6 N5 O
CSKHNYIZBSBQMW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

C GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, C 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, C CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.165
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 105.94 α = 90.00
b = 105.94 β = 90.00
c = 305.48 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-21
  • Released Date: 2012-09-05
  • Deposition author(s): Sun, Q., Chook, Y.M.

Revision History

  • 2013-01-23
    Type: Citation | Details: Citation update
  • 2012-10-17
    Type: Entry title | Details: --