9FDX: Human Sirt2

Crystal structure of human Sirt2 in complex with the peptide-based inhibitor KT9. Determined by X-ray diffraction at 1.55 Å resolution. Released 28 May 2025.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,624
Mol. weight: 35.38 kDa
Ligands: A1IBZ, ZN
Released: 28 May 2025

Explore 9FDX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FDX contains 16 α-helices and 15 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: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	64-71	8
β-strand	79-83	5	1
α-helix	85-87	3
α-helix	89-91	3
α-helix	115-119	5
β-strand	120	1	2
α-helix	121-126	6
α-helix	129-137	9
α-helix	147-157	11
β-strand	161-166	6	1
α-helix	172-175	4
α-helix	180-182	3
β-strand	183-185	3	1
β-strand	188-195	8	3
β-strand	203-205	3	3
α-helix	206-214	9
β-strand	220	1	4
β-strand	227	1	4
β-strand	228-232	5	3
β-strand	235	1	2
α-helix	238-240	3
α-helix	241-250	10
β-strand	256-260	5	1
α-helix	269-275	7
β-strand	282-286	5	1
β-strand	292	1	5
α-helix	293-294	2
β-strand	307	1	5
β-strand	317-321	5	1
α-helix	324-335	12
α-helix	338-353	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacetylase sirtuin-2	A	protein	304	Homo sapiens	Q8IXJ6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9FDX_1 NAD-dependent protein deacetylase sirtuin-2 (chains A)
GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHL
PYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTL
ERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDI
VFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQ
SDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASI
DAQS

Ligands and cofactors

ID	Name	Formula	Copies
A1IBZ	(2~{S})-2-acetamido-~{N}-[(2~{S},3~{R})-1-azanyl-3-oxidanyl-1-oxidanylidene-but…	C22 H32 Cl2 N4 O5 S	1
ZN	Zinc ion	Zn	1

Water and common crystallization additives (EDO, DMS) are not listed.

Primary citation

Efficient Crystallization of Apo Sirt2 for Small-Molecule Soaking and Structural Analysis of Ligand Interactions. Friedrich, F., Schiedel, M., Swyter, S. et al. J Med Chem (2025) 68:10771-10780. DOI 10.1021/acs.jmedchem.4c02896 · PubMed

Other PDB entries of the same protein (UniProt Q8IXJ6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9S1Z 1.1 Å, Crystal structure of human SIRT2 in complex with the covalent adduct of SirReal-triazole…
9FDR 1.25 Å, Crystal structure of human Sirt2 in apo form with opened selectivity pocket
9FDS 1.4 Å, Crystal structure of human Sirt2 in complex with SirReal2
4RMH 1.42 Å, Human Sirt2 in complex with SirReal2 and Ac-Lys-H3 peptide
30KD 1.45 Å, Crystal structure of human SIRT2 in complex with KMyrMe peptide
4RMI 1.45 Å, Human Sirt2 in complex with SirReal1 and Ac-Lys-OTC peptide
9S46 1.45 Å, Human SIRT2 in Complex with RW-78
9S48 1.45 Å, Human SIRT2 in Complex with RW-80
5YQO 1.48 Å, Crystal structure of Sirt2 in complex with selective inhibitor L5C
4X3O 1.5 Å, Sirt2 in complex with a myristoyl peptide
9S20 1.5 Å, Crystal structure of human SIRT2 in complex with SirReal-triazole inhibitor SH10
8QOO 1.55 Å, Crystal structure of human Sirt2 in complex with the peptide-based pseudo-inhibitor…

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