Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 31.22 kDa 
• Atom Count: 2300 
• Modelled Residue Count: 245 
• Deposited Residue Count: 270 
• Unique protein chains: 3

2C2Z

Crystal structure of caspase-8 in complex with aza-peptide Michael acceptor inhibitor

• PDB DOI: 10.2210/pdb2C2Z/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-10-02 Released: 2006-09-20 
• Deposition Author(s): Ganesan, R., Jelakovic, S., Ekici, O.D., Li, Z.Z., James, K.E., Asgian, J.L., Campbell, A.J., Mikolajczyk, J., Salvesen, G.S., Powers, J.C., Gruetter, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.187 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 

Literature

Design, Synthesis, and Evaluation of Aza-Peptide Michael Acceptors as Selective and Potent Inhibitors of Caspases-2, -3, -6, -7, -8, -9, and - 10.

Ekici, O.D., Li, Z.Z., Campbell, A.J., James, K.E., Asgian, J.L., Mikolajczyk, J., Salvesen, G.S., Ganesan, R., Jelakovic, S., Grutter, M.G., Powers, J.C.

(2006) J Med Chem 49: 5728

• PubMed: 16970398 
• DOI: 10.1021/jm0601405
• Primary Citation of Related Structures:  
  2C1E, 2C2K, 2C2M, 2C2O, 2C2Z


• PubMed Abstract: 
  

Aza-peptide Michael acceptors are a novel class of inhibitors that are potent and specific for caspases-2, -3, -6, -7, -8, -9, and -10. The second-order rate constants are in the order of 10(6) M(-1) s(-1). The aza-peptide Michael acceptor inhibitor 18t (Cbz-Asp-Glu-Val-AAsp-trans-CH=CH-CON(CH(2)-1-Naphth)(2) is the most potent compound and it inhibits caspase-3 with a k(2) value of 5620000 M(-1) s(-1). The inhibitor 18t is 13700, 190, 6.4, 594, 37500, and 173-fold more selective for caspase-3 over caspases-2, -6, -7, -8, -9, and -10, respectively. Aza-peptide Michael acceptors designed with caspase specific sequences are selective and do not show any cross reactivity with clan CA cysteine proteases such as papain, cathepsin B, and calpains. High-resolution crystal structures of caspase-3 and caspase-8 in complex with aza-peptide Michael acceptor inhibitors demonstrate the nucleophilic attack on C2 and provide insight into the selectivity and potency of the inhibitors with respect to the P1' moiety.

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Organizational Affiliation: 

School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CASPASE-8 P18 SUBUNIT	A	159	Homo sapiens	Mutation(s): 0  Gene Names: CASP8, MCH5 EC: 3.4.22 (PDB Primary Data), 3.4.22.61 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens) Explore Q14790  Go to UniProtKB:  Q14790
PHAROS:  Q14790

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CASPASE-8 P10 SUBUNIT	B	106	Homo sapiens	Mutation(s): 0  Gene Names: CASP8, MCH5 EC: 3.4.22 (PDB Primary Data), 3.4.22.61 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens) Explore Q14790  Go to UniProtKB:  Q14790
PHAROS:  Q14790

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AZA-PEPTIDE INHIBITOR (5S, 8R, 11S)-8-(2-CARBOXYETHYL) -14-[4-(3,4-DIHYDROQUINOLIN-1(2H)-YL)-4-OXOBUTANOYL] -11-[(1R)-1-HYDROXYETHYL]-5-(2-METHYLPROPYL)-3,6,9,12-TETRAOXO -1-PHENYL-2-OXA-4,7,10,13,14-PENTAAZAHEXADECAN-16-OIC ACID	C	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTD	D [auth B]	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000336	C	Cbz-Leu-Glu-Thr-AAsp-CHCH-CON-tetrahydroquinoline	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.187 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.52	α = 90
b = 62.52	β = 90
c = 129.94	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-02 
• Released Date: 2006-09-20 
Deposition Author(s): Ganesan, R., Jelakovic, S., Ekici, O.D., Li, Z.Z., James, K.E., Asgian, J.L., Campbell, A.J., Mikolajczyk, J., Salvesen, G.S., Powers, J.C., Gruetter, M.G.

Revision History  

• Version 1.0: 2006-09-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2011-07-20
  Changes: Other, Structure summary
• Version 1.3: 2012-11-30
  Changes: Other
• Version 1.4: 2017-02-08
  Changes: Source and taxonomy