9BA9: Protein O-GlcNAcase

O-GlcNAcase (OGA) inhibitor complex for the Treatment of Alzheimer's Disease. Determined by X-ray diffraction at 2.75 Å resolution. Released 15 Jan 2025.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,710
Mol. weight: 61.57 kDa
Ligands: A1AKL
Released: 15 Jan 2025

Explore 9BA9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BA9 contains 27 α-helices and 10 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: 27 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	61-66	6	1
α-helix	71-73	3
α-helix	75-87	13
β-strand	92-95	4	1
α-helix	110-111	2
α-helix	113-128	16
β-strand	132-137	6	1
α-helix	148-163	16
β-strand	168-172	5	1
α-helix	182-187	6
α-helix	191-205	15
β-strand	212-215	4	1
α-helix	221-223	3
α-helix	232-240	9
β-strand	246-249	4	1
α-helix	261-271	11
α-helix	274-275	2
β-strand	276-279	4	1
α-helix	301-306	6
β-strand	309-312	4	1
α-helix	319-321	3
α-helix	322-334	13
α-helix	376-388	13
α-helix	545-548	4
α-helix	551-553	3
α-helix	555-564	10
β-strand	567	1	2
β-strand	570	1	2
α-helix	573-587	15
α-helix	589-592	4
α-helix	602-630	29
α-helix	634-639	6
α-helix	641-662	22
α-helix	669-671	3
α-helix	673-675	3
α-helix	677-680	4
α-helix	685-692	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein O-GlcNAcase	A	protein	535	Homo sapiens	O60502 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9BA9_1 Protein O-GlcNAcase (chains A)
SLGGARRFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYS
VEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALL
FDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSP
YLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLF
LGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTDSEDST
VSIQIKLENEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRQVAHSGAKASVV
DPGPNEKPLYTAEPVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNSKG
KDSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFV
QWLGERSHSSAQFLIGDQEPWAFRGGLAGEFQRLLPIDGANDLFFQPPPLTPTSK

Ligands and cofactors

ID	Name	Formula	Copies
A1AKL	N-{5-[(piperidin-1-yl)methyl]-1,3-thiazol-2-yl}acetamide	C11 H17 N3 O S	1

Primary citation

Discovery and clinical translation of ceperognastat, an O-GlcNAcase (OGA) inhibitor, for the treatment of Alzheimer's disease. Kielbasa, W., Goldsmith, P., Donnelly, K.B. et al. Alzheimers Dement (N Y) (2024) 10:e70020-e70020. DOI 10.1002/trc2.70020 · PubMed

Other PDB entries of the same protein (UniProt O60502 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5UN8 2.13 Å, Crystal Structure of human O-GlcNAcase in complex with glycopeptide p53
5M7U 2.3 Å, Structure of human O-GlcNAc hydrolase with new iminocyclitol type inhibitor
11LJ 2.33 Å, Human oga in complex with ligand 24
5M7R 2.35 Å, Structure of human O-GlcNAc hydrolase
5M7S 2.4 Å, Structure of human O-GlcNAc hydrolase with bound transition state analog ThiametG
7OU6 2.41 Å, Human O-GlcNAc hydrolase in complex with DNJNAc-thiazolidines
5TKE 2.48 Å, Crystal Structure of Eukaryotic Hydrolase
5UN9 2.5 Å, The crystal structure of human O-GlcNAcase in complex with Thiamet-G
8P0L 2.5 Å, Crystal structure of human O-GlcNAcase in complex with an S-linked CKII peptide
9BA8 2.54 Å, O-GlcNAcase (OGA) inhibitor complex for the Treatment of Alzheimer's Disease
2YDQ 2.6 Å, CpOGA D298N in complex with hOGA-derived O-GlcNAc peptide
5M7T 2.6 Å, Structure of human O-GlcNAc hydrolase with PugNAc type inhibitor

Browse structure collections

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