3OZ1 | pdb_00003oz1

cIAP1-BIR3 domain in complex with the Smac-mimetic compound Smac066

PDB DOI: https://doi.org/10.2210/pdb3OZ1/pdb

Classification: APOPTOSIS INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-24 Released: 2010-11-24
Deposition Author(s): Cossu, F., Malvezzi, F., Mastrangelo, E., Canevari, G., Bolognesi, M., Milani, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.257 (Depositor), 0.277 (DCC)
R-Value Work:
0.192 (Depositor), 0.210 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Recognition of Smac-mimetic compounds by the BIR3 domain of cIAP1

Cossu, F., Malvezzi, F., Canevari, G., Mastrangelo, E., Lecis, D., Delia, D., Seneci, P., Scolastico, C., Bolognesi, M., Milani, M.

(2010) Protein Sci

PubMed: 20954235 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.523
Primary Citation Related Structures:
3MUP, 3OZ1

PubMed Abstract:
Inhibitor of apoptosis proteins (IAPs) are negative regulators of apoptosis. As IAPs are overexpressed in many tumors, where they confer chemoresistance, small molecules inactivating IAPs have been proposed as anticancer agents. Accordingly, a number of IAP-binding pro-apoptotic compounds that mimic the sequence corresponding to the N-terminal tetrapeptide of Smac/DIABLO, the natural endogenous IAPs inhibitor, have been developed. Here, we report the crystal structures of the BIR3 domain of cIAP1 in complex with Smac037, a Smac-mimetic known to bind potently to the XIAP-BIR3 domain and to induce degradation of cIAP1, and in complex with the novel Smac-mimetic compound Smac066. Thermal stability and fluorescence polarization assays show the stabilizing effect and the high affinity of both Smac037 and Smac066 for cIAP1- and cIAP2-BIR3 domains.

Organizational Affiliation

Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Via Celoria 26, I-20133, Milano, Italy.

Macromolecule Content

Total Structure Weight: 60.26 kDa
Atom Count: 3,579
Modeled Residue Count: 412
Deposited Residue Count: 488
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baculoviral IAP repeat-containing protein 2	A, B, C, D	122	Homo sapiens	Mutation(s): 0 Gene Names: BIRC2, API1, IAP2, MIHB, RNF48 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q13490 (Homo sapiens) Explore Q13490 Go to UniProtKB: Q13490
PHAROS: Q13490 GTEx: ENSG00000110330
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13490
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BMB Query on BMB Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	(3S,6S,7R,9aS)-7-[2-(benzylamino)ethyl]-N-(diphenylmethyl)-6-{[(2S)-2-(methylamino)butanoyl]amino}-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide C₃₇ H₄₇ N₅ O₃ NVNDSZWHCFDEAR-UCDLYESDSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth D] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C]	E [auth A], G [auth B], I [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.257 (Depositor), 0.277 (DCC)
R-Value Work: 0.192 (Depositor), 0.210 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.589	α = 90
b = 114.63	β = 90
c = 92.962	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-11-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations