9FDR: NAD-dependent protein deacetylase sirtuin-2

Crystal structure of human Sirt2 in apo form with opened selectivity pocket. Determined by X-ray diffraction at 1.25 Å resolution. Released 28 May 2025.

Method: X-ray diffraction
Resolution: 1.25 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,776
Mol. weight: 35.19 kDa
Ligands: ZN
Released: 28 May 2025

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

Secondary structure: helices and β-sheets

9FDR contains 19 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: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	64-72	9
β-strand	79-83	5	1
α-helix	85-87	3
α-helix	89-91	3
α-helix	99-101	3
α-helix	108-110	3
α-helix	115-119	5
β-strand	120	1	2
α-helix	121-126	6
α-helix	129-138	10
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	206-215	10
β-strand	220	1	4
β-strand	227	1	4
β-strand	228-232	5	3
α-helix	233-234	2
β-strand	235	1	2
α-helix	238-240	3
α-helix	241-250	10
β-strand	256-260	5	1
α-helix	270-275	6
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

>9FDR_1 NAD-dependent protein deacetylase sirtuin-2 (chains A)
GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHL
PYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTL
ERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDI
VFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQ
SDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASI
DAQS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (DMS, PG4, EDO, PEG) 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…
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…
8QT1 1.55 Å, Crystal structure of human Sirt2 in complex with the super-slow substrate TNFn-5

Browse structure collections

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