Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.93 kDa 
• Atom Count: 1787 
• Residue Count: 185 
• Unique protein chains: 1

4HY5

Crystal structure of cIAP1 BIR3 bound to T3256336

• DOI: 10.2210/pdb4HY5/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-13 Released: 2013-01-30 
• Deposition Author(s): Dougan, D.R., Snell, G.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.205 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

Design and Synthesis of Potent Inhibitor of Apoptosis (IAP) Proteins Antagonists Bearing an Octahydropyrrolo[1,2-a]pyrazine Scaffold as a Novel Proline Mimetic.

Hashimoto, K., Saito, B., Miyamoto, N., Oguro, Y., Tomita, D., Shiokawa, Z., Asano, M., Kakei, H., Taya, N., Kawasaki, M., Sumi, H., Yabuki, M., Iwai, K., Yoshida, S., Yoshimatsu, M., Aoyama, K., Kosugi, Y., Kojima, T., Morishita, N., Dougan, D.R., Snell, G.P., Imamura, S., Ishikawa, T.

(2013) J Med Chem 56: 1228-1246

• PubMed: 23298277 
• DOI: 10.1021/jm301674z
• Structures With Same Primary Citation


• PubMed Abstract: 
  

To develop novel inhibitor of apoptosis (IAP) proteins antagonists, we designed a bicyclic octahydropyrrolo[1,2-a]pyrazine scaffold as a novel proline bioisostere. This design was based on the X-ray co-crystal structure of four N-terminal amino acid residues (AVPI) of the second mitochondria-derived activator of caspase (Smac) with the X-chromosome-linked IAP (XIAP) protein. Lead optimization of this scaffold to improve oral absorption yielded compound 45, which showed potent cellular IAP1 (cIAP1 IC(50): 1.3 nM) and XIAP (IC(50): 200 nM) inhibitory activity, in addition to potent tumor growth inhibitory activity (GI(50): 1.8 nM) in MDA-MB-231 breast cancer cells. X-ray crystallographic analysis of compound 45 bound to XIAP and to cIAP1 was achieved, revealing the various key interactions that contribute to the higher cIAPI affinity of compound 45 over XIAP. Because of its potent IAP inhibitory activities, compound 45 (T-3256336) caused tumor regression in a MDA-MB-231 tumor xenograft model (T/C: -53% at 30 mg/kg).

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Organizational Affiliation: 

Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Baculoviral IAP repeat-containing protein 2	A, B	115	Homo sapiens	Mutation(s): 0  Gene Names: API1, BIRC2, IAP2, MIHB, RNF48 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q13490 (Homo sapiens) Go to UniProtKB:  Q13490
NIH Common Fund Data Resources
PHAROS  Q13490 GTEx  ENSG00000110330

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1AQ	A, B	(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
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001138 (1AQ)	A, B	(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		--

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1AQ	IC50 :  1.2999999523162842   nM  PDBBind
1AQ	IC50:  1.2999999523162842   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.205 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.106	α = 90
b = 68.176	β = 90
c = 122.31	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-13 
• Released Date: 2013-01-30 
Deposition Author(s): Dougan, D.R., Snell, G.P.

Revision History 

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2013-02-27
  Changes: Database references
• Version 1.2: 2013-08-07
  Changes: Non-polymer description, Structure summary
• Version 1.3: 2015-09-09
  Changes: Structure summary