3L9H: Kinesin-like protein KIF11

X-ray structure of mitotic kinesin-5 (KSP, KIF11, Eg5)in complex with the hexahydro-2H-pyrano[3,2-c]quinoline EMD 534085. Determined by X-ray diffraction at 2.0 Å resolution. Released 2 Mar 2010.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,603
Mol. weight: 83.92 kDa
Ligands: ADP, EMQ
Released: 2 Mar 2010

Explore 3L9H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3L9H contains 39 α-helices and 40 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: 20 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	1
α-helix	19	1
β-strand	20-25	6	2
α-helix	30-33	4
α-helix	37-38	2
β-strand	39	1	3
β-strand	41-44	4	4
β-strand	49-56	8	4
β-strand	61-67	7	4
β-strand	70-72	3	2
α-helix	78-81	4
α-helix	82-86	5
α-helix	87-94	8
β-strand	98-105	8	2
α-helix	111-115	5
β-strand	117	1	5
α-helix	119-120	2
α-helix	121-123	3
β-strand	133	1	5
α-helix	135-146	12
β-strand	153-164	12	2
β-strand	167-170	4	2
β-strand	181-182	2	2
β-strand	183-186	4	6
β-strand	194-197	4	6
β-strand	202-203	2	2
α-helix	207-209	3
α-helix	210-227	18
α-helix	231-234	4
β-strand	236-248	13	2
β-strand	254-265	12	2
α-helix	266-268	3
α-helix	290-303	14
α-helix	311-313	3
α-helix	315-319	5
α-helix	321-323	3
β-strand	329-336	8	2
β-strand	339	1	3
α-helix	340-342	3
α-helix	343-356	14
β-strand	360-361	2	1

Chain B: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	17	1
β-strand	18	1	7
α-helix	19	1
β-strand	20-25	6	8
α-helix	26-28	3
α-helix	30-34	5
β-strand	41-44	4	9
β-strand	49-56	8	9
β-strand	61-67	7	9
β-strand	70-72	3	8
α-helix	78-81	4
α-helix	82-86	5
α-helix	87-94	8
β-strand	98-104	7	8
α-helix	111-115	5
β-strand	117	1	10
α-helix	127-129	3
β-strand	133	1	10
α-helix	135-146	12
β-strand	152-164	13	8
β-strand	167-170	4	8
β-strand	182	1	8
β-strand	183-186	4	11
β-strand	194-197	4	11
β-strand	202-204	3	8
α-helix	210-227	18
α-helix	231-234	4
β-strand	236-248	13	8
β-strand	254-265	12	8
α-helix	266-268	3
α-helix	290-304	15
α-helix	311-313	3
α-helix	315-319	5
α-helix	321-323	3
β-strand	329-336	8	8
α-helix	340-342	3
α-helix	343-356	14
β-strand	360	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinesin-like protein KIF11	A, B	protein	368	Homo sapiens	P52732 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3L9H_1 Kinesin-like protein KIF11 (chains A, B)
MASQPNSSAKKKEEKGKNIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADK
SSRKTYTFDMVFGASTKQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEGERS
PNEEYTWEEDPLAGIIPRTLHQIFEKLTDNGTEFSVKVSLLEIYNEELFDLLNPSSDVSE
RLQMFDDPRNKRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFS
VTIHMKETTIDGEELVKIGKLNLVDLAGSENIGRSGAVDKRAREAGNINQSLLTLGRVIT
ALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAKNIL
NKPEVNQK

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
EMQ	1-[2-(dimethylamino)ethyl]-3-{[(2R,4aS,5R,10bS)-5-phenyl-9-(trifluoromethyl)-3,…	C25 H31 F3 N4 O2	2

Primary citation

The discovery and optimization of hexahydro-2H-pyrano[3,2-c]quinolines (HHPQs) as potent and selective inhibitors of the mitotic kinesin-5. Schiemann, K., Finsinger, D., Zenke, F. et al. Bioorg Med Chem Lett (2010) 20:1491-1495. DOI 10.1016/j.bmcl.2010.01.110 · PubMed

Other PDB entries of the same protein (UniProt P52732 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZCW 1.69 Å, Eg5 - New allosteric binding site
6TLE 1.75 Å, Human Eg5 motor domain mutant E344K
1X88 1.8 Å, Human Eg5 motor domain bound to Mg-ADP and monastrol
6G6Y 1.8 Å, Eg5-inhibitor complex
2PG2 1.85 Å, Crystal structure of KSP in complex with ADP and thiophene containing inhibitor 15
1Q0B 1.9 Å, Crystal structure of the motor protein KSP in complex with ADP and monastrol
2X7C 1.9 Å, Crystal structure of human kinesin Eg5 in complex with (S)-enastron
8YHH 1.95 Å, The Crystal Structure of Mitotic Kinesin Eg5 from Biortus
3K5E 1.97 Å, The structure of human kinesin-like motor protein Kif11/KSP/Eg5 in complex with ADP and…
2WOG 2.0 Å, Intermediate and final states of human kinesin Eg5 in complex with S-trityl-L-cysteine
5JV3 2.01 Å, The neck-linker and alpha 7 helix of Homo sapiens Eg5 fused to EB1
1II6 2.1 Å, Crystal Structure of the Mitotic Kinesin Eg5 in Complex with Mg-ADP.

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