8VA5: Menin mutant - T349M

Menin mutant - T349M in complex with Ziftomenib (KO-539). Determined by X-ray diffraction at 1.3 Å resolution. Released 20 Nov 2024.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Homo sapiens
Chains: 1
Atoms: 4,658
Mol. weight: 55.97 kDa
Ligands: K5O
Released: 20 Nov 2024

Explore 8VA5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VA5 contains 31 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: 31 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
β-strand	13	1	1
α-helix	16-27	12
α-helix	34-45	12
α-helix	46-50	5
β-strand	81	1	1
α-helix	83-100	18
α-helix	103-105	3
α-helix	109-111	3
α-helix	115-127	13
α-helix	143-149	7
α-helix	154-167	14
β-strand	174-177	4	2
β-strand	182-186	5	2
α-helix	188-190	3
β-strand	192-194	3	2
α-helix	203-205	3
α-helix	212-216	5
α-helix	220-225	6
β-strand	228-229	2	2
α-helix	232-241	10
β-strand	246-248	3	3
β-strand	251-252	2	3
α-helix	254-269	16
α-helix	277-289	13
α-helix	291-292	2
α-helix	298-312	15
α-helix	319-330	12
α-helix	334-348	15
α-helix	358-366	9
α-helix	367-371	5
α-helix	372-384	13
α-helix	403-405	3
α-helix	407-424	18
α-helix	434-445	12
α-helix	449-452	4
β-strand	456-457	2	4
β-strand	550-551	2	4
α-helix	556-561	6
α-helix	562-564	3
α-helix	572-580	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Menin	A	protein	489	Homo sapiens	O00255 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8VA5_1 Menin (chains A)
GGSSSMGLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVGL
TYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKKVSDVIWNSLSRSYFK
DRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAE
VTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLE
LLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYHKGIASAKTYYRD
EHIYPYMYLAGYHCRNRNVREALQAWADMATVIQDYNYCREDEEIYKEFFEVANDVIPNL
LKEAASLLEAGSQGSALQDPECFAHLLRFYDGICKWEEGSPTPVLHVGWATFLVQSLGRF
EGQVRQKVRIVSVPAPTASPPPEGPVLTFQSEKMKGMKELLVATKINSSAIKLQLTAQSQ
VQMKKQKVS

Ligands and cofactors

ID	Name	Formula	Copies
K5O	Ziftomenib	C33 H42 F3 N9 O2 S2	1

Water and common crystallization additives (DMS, EDO, PG4, PEG) are not listed.

Primary citation

Ziftomenib in relapsed or refractory acute myeloid leukaemia (KOMET-001): a multicentre, open-label, multi-cohort, phase 1 trial. Wang, E.S., Issa, G.C., Erba, H.P. et al. Lancet Oncol (2024) 25:1310-1324. DOI 10.1016/S1470-2045(24)00386-3 · PubMed

Other PDB entries of the same protein (UniProt O00255 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O5I 1.24 Å, Menin in complex with MI-3454
4GQ4 1.27 Å, Human menin with bound inhibitor MI-2-2
9C4Y 1.31 Å, Menin mutant - T349M
9C4W 1.4 Å, Menin mutant - G331R
9C4Z 1.4 Å, Menin mutant - G331D
4OG4 1.45 Å, Human menin with bound inhibitor MIV-3S
4GPQ 1.46 Å, Structural insights into inhibition of the bivalent menin-MLL interaction by small…
9C4T 1.46 Å, menin mutant M327I in complex with MLL peptide
9C4V 1.47 Å, Menin mutant G331D in complex with MLL peptide
4OG6 1.49 Å, Human menin with bound inhibitor MIV-4
5DB0 1.5 Å, Menin in complex with MI-352
9WN9 1.5 Å, Wild-type Menin complexed with DSP-5336

Browse structure collections

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