9Z6D: LIMK1 mutant D460N

Crystal structure of LIMK1 mutant D460N bound to small molecule inhibitor cLIMK1i. Determined by X-ray diffraction at 1.94 Å resolution. Released 29 Jul 2026.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,640
Mol. weight: 73.31 kDa
Ligands: A1C13
Released: 29 Jul 2026

Explore 9Z6D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Z6D contains 30 α-helices and 28 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: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	332-334	3	1
α-helix	336-338	3
β-strand	339-347	9	1
β-strand	352-358	7	1
β-strand	364-369	6	1
α-helix	375-389	15
β-strand	396	1	2
α-helix	397-398	2
β-strand	399-403	5	1
β-strand	410-414	5	1
β-strand	420	1	2
α-helix	421-426	6
α-helix	434-453	20
β-strand	456-457	2	3
β-strand	466-468	3	2
β-strand	474-476	3	2
β-strand	483-484	2	3
α-helix	513-515	3
α-helix	518-521	4
α-helix	529-544	16
β-strand	555	1	4
β-strand	561	1	4
α-helix	563-569	7
α-helix	576	1
α-helix	579-586	8
α-helix	591-593	3
α-helix	595-596	2
α-helix	597-611	15
α-helix	618-632	15

Chain B: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	332-334	3	5
α-helix	336-338	3
β-strand	339-346	8	5
β-strand	352-358	7	5
β-strand	364-369	6	5
α-helix	376-388	13
β-strand	396	1	6
α-helix	397-398	2
β-strand	399-403	5	5
β-strand	410-414	5	5
β-strand	420	1	6
α-helix	421-426	6
α-helix	434-453	20
β-strand	456-457	2	7
β-strand	466-468	3	6
β-strand	474-476	3	6
β-strand	483-484	2	7
α-helix	513-515	3
α-helix	518-521	4
α-helix	529-544	16
β-strand	555	1	8
β-strand	561	1	8
α-helix	563-569	7
α-helix	575-576	2
α-helix	579-586	8
α-helix	591-593	3
α-helix	595-596	2
α-helix	597-613	17
α-helix	619-631	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LIM domain kinase 1	A, B	protein	313	Homo sapiens	P53667 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9Z6D_1 LIM domain kinase 1 (chains A, B)
GRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKV
MRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASG
MAYLHSMNIIHRNLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDRKKRY
TVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFL
DRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRG
FWETYRRGESGLP

Ligands and cofactors

ID	Name	Formula	Copies
A1C13	N-(3'-methyl-5'-{[4-(trifluoromethyl)pyrimidin-2-yl]amino}[1,1'-biphenyl]-4-yl)…	C21 H17 F3 N4 O	2

Primary citation

A covalent inhibitor targeting Cys-349 of LIMK1 confers selectivity over LIMK2. Patteson, J.B., Manolaridis, I., Hong, M.R. et al. J Biol Chem (2026) 302:113322-113322. DOI 10.1016/j.jbc.2026.113322 · PubMed

Other PDB entries of the same protein (UniProt P53667 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3S95 1.65 Å, Crystal structure of the human LIMK1 kinase domain in complex with staurosporine
8AAU 1.74 Å, LIM Domain Kinase 1 (LIMK1) bound to LIMKi3
6WLY 1.9 Å, PAK4 kinase domain in complex with LIMK1 Thr508 substrate peptide
5HVJ 2.2 Å, Crystal structure of LIMK1 D460N mutant in complex with AMP-PNP
5NXC 2.25 Å, LIM Domain Kinase 1 (LIMK1) In Complex With PF-00477736
9Z6E 2.26 Å, Crystal structure of apo LIMK1 mutant D460N
5L6W 2.53 Å, Structure Of the LIMK1-ATPgammaS-CFL1 Complex
7ATS 2.8 Å, The LIMK1 Kinase Domain Bound To LIJTF500127
7ATU 2.8 Å, The LIMK1 Kinase Domain Bound To LIJTF500025
7B8W 2.8 Å, Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470
5HVK 3.5 Å, Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1

Browse structure collections

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