2YK9: Tricyclic series of Hsp90 inhibitors

Name: PDB 2YK9: Tricyclic series of Hsp90 inhibitors
Published: 2011-10-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Tricyclic series of Hsp90 inhibitors. Determined by X-ray diffraction at 1.32 Å resolution. Released 26 Oct 2011.

Method: X-ray diffraction
Resolution: 1.32 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 1,965
Mol. weight: 23.66 kDa
Ligands: YK9
Released: 26 Oct 2011

Explore 2YK9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YK9 contains 11 α-helices and 8 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	18-21	4	1
α-helix	22-23	2
α-helix	24-35	12
α-helix	43-65	23
α-helix	67-70	4
β-strand	78-83	6	1
β-strand	88-93	6	1
α-helix	100-101	2
α-helix	102-106	5
α-helix	107-123	17
α-helix	128-134	7
α-helix	137-143	7
β-strand	145-153	9	1
β-strand	160-164	5	1
β-strand	169-174	6	1
β-strand	183-190	8	1
α-helix	192-198	7
α-helix	200-210	11
β-strand	218-220	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heat shock protein hsp 90-alpha	A	protein	209	HOMO SAPIENS	P07900 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2YK9_1 HEAT SHOCK PROTEIN HSP 90-ALPHA (chains A)
GHMETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDSGK
ELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQF
GVGFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQ
TEYLEERRIKEIVKKHSQFIGYPITLFVE

Ligands and cofactors

ID	Name	Formula	Copies
YK9	4-(1H-IMIDAZO[4,5-c]pyridin-2-yl)fluoren-9-one	C19 H11 N3 O	1

Primary citation

Tricyclic Series of Heat Shock Protein 90 (Hsp90) Inhibitors Part I: Discovery of Tricyclic Imidazo[4,5-C]Pyridines as Potent Inhibitors of the Hsp90 Molecular Chaperone. Vallee, F., Carrez, C., Pilorge, F. et al. J Med Chem (2011) 54:7206. DOI 10.1021/JM200784M · PubMed

Other PDB entries of the same protein (UniProt P07900 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TN5 1.17 Å, Rapid optimisation of fragments and hits to lead compounds from screening of crude…
5J80 1.17 Å, Crystal Structure of Apo Hsp90-alpha N-domain L107A mutant
3T0H 1.2 Å, Structure insights into mechanisms of ATP hydrolysis and the activation of human Hsp90
5J2X 1.22 Å, Crystal Structure of Hsp90-alpha N-domain in complex with…
3T10 1.24 Å, HSP90 N-terminal domain bound to ACP
6TN4 1.27 Å, Rapid optimisation of fragments and hits to lead compounds from screening of crude…
3WHA 1.3 Å, Hsp90 alpha N-terminal domain in complex with a tricyclic inhibitor
5XRD 1.3 Å, Crystal Structure of the human Hsp90-alpha N-domain bound to the hsp90 inhibitor FS7
5LRL 1.33 Å, Crystal structure of HSP90 in complex with A003492875
6GR5 1.34 Å, Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) variant…
3B28 1.35 Å, Hsp90 alpha N-terminal domain in complex with an inhibitor CH5015765
5J64 1.38 Å, Crystal Structure of Hsp90-alpha N-domain in complex with…

Browse structure collections

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