Crystal structure of XIAP BIR3 with T3256336

Experimental Data Snapshot

  • Resolution: 2.84 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 

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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

  • DOI: https://doi.org/10.1021/jm301674z
  • Primary Citation of Related Structures:  
    4HY0, 4HY4, 4HY5

  • 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).

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase XIAP
A, B, C, D, E
A, B, C, D, E, F, G, H
125Homo sapiensMutation(s): 0 
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens)
Explore P98170 
Go to UniProtKB:  P98170
GTEx:  ENSG00000101966 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98170
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1AQ

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
K [auth A]
N [auth B]
P [auth C]
BA [auth G],
DA [auth H],
K [auth A],
N [auth B],
P [auth C],
S [auth D],
V [auth E],
Y [auth F]
C31 H45 F2 N5 O5
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
I [auth A]
J [auth A]
L [auth B]
AA [auth G],
CA [auth H],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
O [auth C],
Q [auth D],
R [auth D],
T [auth E],
U [auth E],
W [auth F],
X [auth F],
Z [auth G]
Binding Affinity Annotations 
IDSourceBinding Affinity
1AQ BindingDB:  4HY0 IC50: 200 (nM) from 1 assay(s)
PDBBind:  4HY0 IC50: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.84 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.336α = 90
b = 100.84β = 90
c = 184.583γ = 90
Software Package:
Software NamePurpose
ALS-BOSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: 2024-02-28
    Changes: Data collection, Database references, Derived calculations