3B28: Hsp90 alpha N-terminal domain

Hsp90 alpha N-terminal domain in complex with an inhibitor CH5015765. Determined by X-ray diffraction at 1.35 Å resolution. Released 14 Sept 2011.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,254
Mol. weight: 52.41 kDa
Ligands: MG, B2X
Released: 14 Sept 2011

Explore 3B28 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3B28 contains 23 α-helices and 16 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: 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	100-108	9
α-helix	115-122	8
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	195-198	4
α-helix	200-210	11
β-strand	218-220	3	1
α-helix	221-223	3

Chain B: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	18-21	4	2
α-helix	22-23	2
α-helix	24-35	12
α-helix	41-43	3
α-helix	44-65	22
α-helix	67-70	4
β-strand	78-83	6	2
β-strand	88-93	6	2
α-helix	100-108	9
α-helix	111-123	13
α-helix	128-134	7
α-helix	137-143	7
β-strand	145-153	9	2
β-strand	160-164	5	2
β-strand	169-174	6	2
β-strand	183-190	8	2
α-helix	192-198	7
α-helix	200-210	11
β-strand	218-220	3	2
α-helix	221-223	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heat shock protein HSP 90-alpha	A, B	protein	229	Homo sapiens	P07900 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3B28_1 Heat shock protein HSP 90-alpha (chains A, B)
MDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDP
SKLDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGAD
ISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVI
LHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEAE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
B2X	4-(5-chloro-1H,3H-benzo[de]isochromen-6-yl)-6-(methylsulfanyl)-1,3,5-triazin-2-…	C16 H13 Cl N4 O S	2

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

Primary citation

Lead generation of heat shock protein 90 inhibitors by a combination of fragment-based approach, virtual screening, and structure-based drug design. Miura, T., Fukami, T.A., Hasegawa, K. et al. Bioorg Med Chem Lett (2011) 21:5778-5783. DOI 10.1016/j.bmcl.2011.08.001 · 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
2YK9 1.32 Å, Tricyclic series of Hsp90 inhibitors
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…
5J64 1.38 Å, Crystal Structure of Hsp90-alpha N-domain in complex with…

Browse structure collections

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