2YIY: Compound 8

Crystal structure of compound 8 bound to TAK1-TAB. Determined by X-ray diffraction at 2.49 Å resolution. Released 23 May 2012.

Method: X-ray diffraction
Resolution: 2.49 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 2,568
Mol. weight: 35.23 kDa
Ligands: YIY
Released: 23 May 2012

Explore 2YIY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YIY contains 19 α-helices and 14 β-strands across 1 chain. 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: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	1
α-helix	33-35	3
β-strand	37-43	7	1
β-strand	49-54	6	1
β-strand	59-64	6	1
α-helix	68-70	3
α-helix	71-81	11
β-strand	89	1	2
β-strand	92-97	6	1
β-strand	100-105	6	1
β-strand	111	1	2
α-helix	112-117	6
β-strand	122-123	2	3
α-helix	124	1
α-helix	127-145	19
α-helix	159-161	3
β-strand	162-165	4	2
β-strand	170-173	4	2
α-helix	193-195	3
α-helix	198-201	4
α-helix	209-224	16
α-helix	236-244	9
α-helix	249-250	2
β-strand	251-252	2	4
α-helix	257-266	10
α-helix	271-273	3
α-helix	275-276	2
α-helix	277-287	11
α-helix	288-290	3
β-strand	301-302	2	3
α-helix	471-473	3
β-strand	477-478	2	4
α-helix	485-494	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase kinase kinase 7, tgf-beta-activated kinase 1 and MAP3K7-binding…	A	protein	307	HOMO SAPIENS	O43318 (AlphaFold model), Q15750 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2YIY_1 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7, TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1 (chains A)
SLHMIDYKEIEVEEVVGRGAFGVVCKAKWRAKDVAIKQIESESERKAFIVELRQLSRVNH
PNIVKLYGACLNPVCLVMEYAEGGSLYNVLHGAEPLPYYTAAHAMSWCLQCSQGVAYLHS
MQPKALIHRDLKPPNLLLVAGGTVLKICDFGTACDIQTHMTNNKGSAAWMAPEVFEGSNY
SEKCDVFSWGIILWEVITRRKPFDEIGGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRC
WSKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQHSLPPGEDGRVEPYVDFAEFYRL
WSVDHGE

Ligands and cofactors

ID	Name	Formula	Copies
YIY	(1E)-1-[5-tert-butyl-2-(3-fluorophenyl)-1H-pyrazol-3-ylidene]-3-(4-pyridin-3-yl…	C25 H24 F N5 O2	1

Primary citation

The Discovery and Synthesis of Selective Dfg-Out Tak-1 Inhibitors. Green, M.P., Bell, A., Bess, K. et al. To be published.

Other PDB entries of the same protein (UniProt O43318 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7NTH 1.97 Å, Structure of TAK1 in complex with compound 54
7NTI 1.98 Å, Structure of TAK1 in complex with compound 22
2EVA 2.0 Å, Structural Basis for the Interaction of TAK1 Kinase with its Activating Protein TAB1
5JGA 2.0 Å, Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 11c
5V5N 2.01 Å, Crystal structure of Takinib bound to TAK1
8GW3 2.05 Å, Crystal structure of human TAK1 kinase domain fused with TAB1
5E7R 2.11 Å, Crystal structure of TL10-81 bound to TAK1-TAB1
4GS6 2.2 Å, Irreversible Inhibition of TAK1 Kinase by 5Z-7-Oxozeaenol
5JH6 2.37 Å, Crystal structure of TL10-92 bound to TAK1-TAB1
5J7S 2.37 Å, Crystal structure of SM1-71 bound to TAK1-TAB1
5JK3 2.37 Å, Crystal structure of TL11-128 bound to TAK1-TAB1
4O91 2.39 Å, Crystal Structure of type II inhibitor NG25 bound to TAK1-TAB1

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