5M6N | pdb_00005m6n

Small Molecule inhibitors of IAP

PDB DOI: https://doi.org/10.2210/pdb5M6N/pdb

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-10-25 Released: 2017-05-24
Deposition Author(s): Williams, P.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.203 (Depositor), 0.200 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of a Potent Nonpeptidomimetic, Small-Molecule Antagonist of Cellular Inhibitor of Apoptosis Protein 1 (cIAP1) and X-Linked Inhibitor of Apoptosis Protein (XIAP).

Tamanini, E., Buck, I.M., Chessari, G., Chiarparin, E., Day, J.E.H., Frederickson, M., Griffiths-Jones, C.M., Hearn, K., Heightman, T.D., Iqbal, A., Johnson, C.N., Lewis, E.J., Martins, V., Peakman, T., Reader, M., Rich, S.J., Ward, G.A., Williams, P.A., Wilsher, N.E.

(2017) J Med Chem 60: 4611-4625

PubMed: 28492317 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.6b01877
Primary Citation of Related Structures:
5M6E, 5M6F, 5M6H, 5M6L, 5M6M, 5M6N

PubMed Abstract:
XIAP and cIAP1 are members of the inhibitor of apoptosis protein (IAP) family and are key regulators of anti-apoptotic and pro-survival signaling pathways. Overexpression of IAPs occurs in various cancers and has been associated with tumor progression and resistance to treatment. Structure-based drug design (SBDD) guided by structural information from X-ray crystallography, computational studies, and NMR solution conformational analysis was successfully applied to a fragment-derived lead resulting in AT-IAP, a potent, orally bioavailable, dual antagonist of XIAP and cIAP1 and a structurally novel chemical probe for IAP biology.

Organizational Affiliation

Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.

Macromolecule Content

Total Structure Weight: 28.97 kDa
Atom Count: 2,065
Modelled Residue Count: 192
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baculoviral IAP repeat-containing protein 2	A, B	118	Homo sapiens	Mutation(s): 0 Gene Names: BIRC2, API1, MIHB, RNF48 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13490
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7H9 Query on 7H9 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	1-[6-[(4-fluorophenyl)methyl]-3,3-dimethyl-2~{H}-pyrrolo[3,2-b]pyridin-1-yl]-2-[(2~{R},5~{R})-5-methyl-2-[[(3~{R})-3-methylmorpholin-4-yl]methyl]piperazin-4-ium-1-yl]ethanone C₂₉ H₄₁ F N₅ O₂ XIQKDUKFFKQZAO-DNRQZRRGSA-O		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]