5M6N: Small Molecule inhibitors of IAP

Name: PDB 5M6N: Small Molecule inhibitors of IAP
Published: 2017-05-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: apoptosis

Small Molecule inhibitors of IAP. Determined by X-ray diffraction at 1.8 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,065
Mol. weight: 28.97 kDa
Ligands: 7H9, ZN
Released: 24 May 2017

Explore 5M6N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M6N contains 13 α-helices and 8 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	263-268	6
α-helix	269-272	4
α-helix	281-286	6
β-strand	289-291	3	1
β-strand	298-300	3	1
β-strand	306-307	2	1
α-helix	316-323	8
β-strand	327	1	2
α-helix	328-334	7
α-helix	336-342	7
α-helix	349-355	7

Chain B: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	263-268	6
α-helix	269-272	4
α-helix	281-286	6
β-strand	289-291	3	3
β-strand	294	1	2
β-strand	298-300	3	3
β-strand	306-307	2	3
α-helix	316-323	8
α-helix	328-334	7
α-helix	336-345	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Baculoviral IAP repeat-containing protein 2	A, B	protein	118	Homo sapiens	Q13490 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5M6N_1 Baculoviral IAP repeat-containing protein 2 (chains A, B)
MGSSHHHHHHSSGLVPRGSHMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVK
CFCCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRYPHLLEQLLSTS

Ligands and cofactors

ID	Name	Formula	Copies
7H9	1-[6-[(4-fluorophenyl)methyl]-3,3-dimethyl-2~{H}-pyrrolo[3,2-b]pyridin-1-yl]-2-…	C29 H41 F N5 O2	2
ZN	Zinc ion	Zn	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

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. et al. J Med Chem (2017) 60:4611-4625. DOI 10.1021/acs.jmedchem.6b01877 · PubMed

Other PDB entries of the same protein (UniProt Q13490 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HY4 1.25 Å, Crystal structure of cIAP1 BIR3 bound to T3170284
7QGJ 1.3 Å, Apo structure of BIR2 Domain of BIRC2
3D9T 1.5 Å, CIAP1-BIR3 in complex with N-terminal peptide from Caspase-9 (ATPFQE)
8DSF 1.5 Å, Structure of cIAP1 with BCCov
4KMN 1.52 Å, Structure of cIAP1-BIR3 and inhibitor
4LGE 1.55 Å, Crystal structure of clAP1 BIR3 bound to T3261256
6HPR 1.7 Å, Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub
7TRL 1.74 Å, Crystal structure of human BIRC2 BIR3 domain in complex with histone H3
4HY5 1.75 Å, Crystal structure of cIAP1 BIR3 bound to T3256336
3UW4 1.79 Å, Crystal structure of cIAP1 BIR3 bound to GDC0152
4MU7 1.79 Å, Crystal structure of cIAP1 BIR3 bound to T3450325
9N23 1.8 Å, Crystal structure of cIAP1-BIR3 with XB2 series SMAC mimetic ligand

Browse structure collections

About this viewer

MolViewer shows 5M6N directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.