2PG2: KSP

Crystal structure of KSP in complex with ADP and thiophene containing inhibitor 15. Determined by X-ray diffraction at 1.85 Å resolution. Released 5 Jun 2007.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,776
Mol. weight: 83.74 kDa
Ligands: K01, ADP, MG
Released: 5 Jun 2007

Explore 2PG2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PG2 contains 42 α-helices and 38 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: 21 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
α-helix	19	1
β-strand	20-25	6	2
α-helix	26-28	3
α-helix	30-34	5
β-strand	41-44	4	3
β-strand	49-53	5	3
β-strand	63-67	5	3
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	4
α-helix	119-120	2
α-helix	121-123	3
β-strand	133	1	4
α-helix	135-149	15
β-strand	152-164	13	2
β-strand	167-170	4	2
β-strand	182	1	2
β-strand	183-186	4	5
β-strand	194-197	4	5
α-helix	199-201	3
β-strand	202-204	3	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	290-304	15
α-helix	311-313	3
α-helix	315-319	5
α-helix	321-323	3
β-strand	329-336	8	2
α-helix	340-342	3
α-helix	343-356	14
β-strand	360	1	1

Chain B: 21 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	6
β-strand	20-25	6	7
α-helix	26-28	3
α-helix	30-34	5
α-helix	37-39	3
β-strand	41-44	4	8
β-strand	49-56	8	8
β-strand	61-67	7	8
β-strand	70-72	3	7
α-helix	78-81	4
α-helix	82-86	5
α-helix	87-94	8
β-strand	98-104	7	7
α-helix	111-115	5
β-strand	117	1	9
α-helix	119-120	2
α-helix	121-123	3
α-helix	127-129	3
β-strand	133	1	9
α-helix	135-146	12
β-strand	153-164	12	7
β-strand	167-170	4	7
β-strand	182	1	7
β-strand	183-186	4	10
β-strand	194-197	4	10
β-strand	202-203	2	7
α-helix	207-209	3
α-helix	210-227	18
α-helix	231-234	4
β-strand	236-248	13	7
β-strand	254-265	12	7
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	7
α-helix	340-342	3
α-helix	343-356	14
β-strand	360-361	2	6

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

>2PG2_1 Kinesin-like protein KIF11 (chains A, B)
MASQPNSSAKKKEEKGKNIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADK
SSRKTYTFDMVFGASTKQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEGERS
PNEEYTWEEDPLAGIIPRTLHQIFEKLTDNGTEFSVKVSLLEIYNEELFDLLNPSSDVSE
RLQMFDDPRNKRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFS
VTIHMKETTIDGEELVKIGKLNLVDLAGSENIGRSGAVDKRAREAGNINQSLLTLGRVIT
ALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAKNIL
NKPEVNQK

Ligands and cofactors

ID	Name	Formula	Copies
K01	N,n-diethyl-2-[(2-thienylcarbonyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-…	C18 H22 N2 O2 S2	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	2

Primary citation

Synthesis and SAR of thiophene containing kinesin spindle protein (KSP) inhibitors. Pinkerton, A.B., Lee, T.T., Hoffman, T.Z. et al. Bioorg Med Chem Lett (2007) 17:3562-3569. DOI 10.1016/j.bmcl.2007.04.076 · 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
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
3L9H 2.0 Å, X-ray structure of mitotic kinesin-5 (KSP, KIF11, Eg5)in complex with the…
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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