4HY0

Crystal structure of XIAP BIR3 with T3256336

Structural Biology Knowledgebase: 4HY0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.208

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HY0

Classification: LIGASE / LIGASE INHIBITOR

Total Structure Weight: 119423.75

Macromolecule Entities
Molecule Chains Length Organism Details
E3 ubiquitin-protein ligase XIAP A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 125 Homo sapiens EC#: 6.3.2 IUBMB
Gene Name(s): XIAP Gene View API3 BIRC4 IAP3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1AQ
Query on 1AQ

A, B, C, D, E, F, G, H (3S,7R,8aR)-2-{(2S)-2-(4,4-difluorocyclohexyl)- 2-[(N-methyl-L-alanyl)amino]acetyl}-N-[(4R)- 3,4-dihydro-2H-chromen-4-yl]-7-ethoxyoctahydropyrrolo[1,2- a]pyrazine-3-carboxamide
C31 H45 F2 N5 O5
WQLHYSFOEZZZDD-QAPMSZJWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D, E, F, G, H ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1AQ IC50: 200 nM (98) BindingDB

N/A in BindingMoad
IC50: 200 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_001138 (1XY,1Y3,1Y2,MAA) A, B, C, D, E, F, H (3S,7R,8AR)-2-{(2S)-2-(4,4-DIFLUOROCYCLOHEXYL)-2-[(N-METHYL-L-ALANYL)AMINO]ACETYL}-N-[(4R)-3,4-DIHYDRO-2H-CHROMEN-4-YL]-7-ETHOXYOCTAHYDROPYRROLO[1,2-A]PYRAZINE-3-CARBOXAMIDE Peptide-like /
Antagonist
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.208
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.34 α = 90.00
b = 100.84 β = 90.00
c = 184.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-12
  • Released Date: 2013-01-30
  • Deposition author(s): Snell, G.S., Dougan, D.R.

Revision History

  • 2013-08-07
    Type: Function and keywords | Details: Indicate that this is an inhibited complex
  • 2013-08-07
    Type: Non-polymer description | Details: Add subcomponents to 1AQ
  • 2013-02-27
    Type: Citation | Details: Citation update