9BA8: Protein O-GlcNAcase

O-GlcNAcase (OGA) inhibitor complex for the Treatment of Alzheimer's Disease. Determined by X-ray diffraction at 2.54 Å resolution. Released 15 Jan 2025.

Method: X-ray diffraction
Resolution: 2.54 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,366
Mol. weight: 115.53 kDa
Ligands: A1AKM
Released: 15 Jan 2025

Explore 9BA8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BA8 contains 53 α-helices and 24 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: 26 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	61-66	6	1
α-helix	72-74	3
α-helix	75-87	13
β-strand	92-95	4	1
α-helix	110-112	3
α-helix	113-128	16
β-strand	132-137	6	1
α-helix	148-163	16
β-strand	168-172	5	1
α-helix	179-181	3
α-helix	182-185	4
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
β-strand	259	1	2
α-helix	261-271	11
β-strand	276-279	4	1
α-helix	295-296	2
β-strand	299	1	2
α-helix	301-306	6
β-strand	309-312	4	1
α-helix	318-321	4
α-helix	322-332	11
α-helix	376-389	14
α-helix	545-548	4
α-helix	551-554	4
α-helix	555-564	10
β-strand	567	1	3
β-strand	570	1	3
α-helix	573-587	15
α-helix	589-592	4
α-helix	602-629	28
α-helix	634-661	28
α-helix	673-675	3
α-helix	677-680	4
α-helix	684-691	8

Chain B: 27 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	61-66	6	4
α-helix	72-74	3
α-helix	75-87	13
β-strand	92-95	4	4
α-helix	110-112	3
α-helix	113-128	16
β-strand	132-137	6	4
α-helix	148-163	16
β-strand	168-172	5	4
α-helix	179-181	3
α-helix	182-185	4
α-helix	191-205	15
β-strand	212-215	4	4
α-helix	221-223	3
α-helix	232-240	9
β-strand	246-249	4	4
β-strand	259	1	5
α-helix	261-271	11
β-strand	276-279	4	4
α-helix	295-296	2
β-strand	299	1	5
α-helix	301-306	6
β-strand	309-312	4	4
α-helix	318-321	4
α-helix	322-332	11
α-helix	376-389	14
α-helix	545-548	4
α-helix	551-553	3
α-helix	555-564	10
β-strand	567	1	6
β-strand	570	1	6
α-helix	573-587	15
α-helix	589-592	4
α-helix	602-629	28
α-helix	634-663	30
α-helix	669-671	3
α-helix	673-675	3
α-helix	677-680	4
α-helix	684-691	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein O-GlcNAcase	A, B	protein	499	Homo sapiens	O60502 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9BA8_1 Protein O-GlcNAcase (chains A, B)
SLGGARRFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYS
VEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALL
FDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSP
YLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLF
LGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNYSPQMALKLALTEWL
QEFGVPHQYSSRQVAHSGAKASVVDPGPNEKPLYTAEPVTLEDLQLLADLFYLPYEHGPK
GAQMLREFQWLRANSSVVSVNSKGKDSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANR
TILYDMYSYVWDIKSIMSMVKSFVQWLGERSHSSAQFLIGDQEPWAFRGGLAGEFQRLLP
IDGANDLFFQPPPLTPTSK

Ligands and cofactors

ID	Name	Formula	Copies
A1AKM	N-[4-fluoro-5-({(2S,4S)-2-methyl-4-[(5-methyl-1,2,4-oxadiazol-3-yl)methoxy]pipe…	C16 H22 F N5 O3 S	2

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
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
5VVO 2.6 Å, Structural Investigations of the Substrate Specificity of Human O-GlcNAcase

Browse structure collections

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