2YDI: Serine/threonine-protein kinase CHK1

Discovery of Checkpoint Kinase Inhibitor AZD7762 by Structure Based Design and Optimization of Thiophene Carboxamide Ureas. Determined by X-ray diffraction at 1.6 Å resolution. Released 4 Apr 2012.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 2,577
Mol. weight: 33.49 kDa
Ligands: YDI
Released: 4 Apr 2012

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

Secondary structure: helices and β-sheets

2YDI contains 14 α-helices and 17 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: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	1
β-strand	21-28	8	1
β-strand	34-41	8	1
α-helix	42-44	3
α-helix	48-59	12
β-strand	67	1	2
β-strand	70-76	7	1
β-strand	79-84	6	1
β-strand	90-91	2	2
α-helix	92-95	4
β-strand	97	1	3
β-strand	101	1	3
α-helix	104-123	20
β-strand	126-127	2	4
α-helix	133-135	3
β-strand	136-138	3	2
β-strand	144-146	3	2
β-strand	153-154	2	4
β-strand	156-157	2	5
β-strand	160-161	2	5
β-strand	164	1	6
α-helix	171-173	3
α-helix	177-180	4
β-strand	184	1	6
α-helix	186-203	18
α-helix	216-222	7
α-helix	231-233	3
α-helix	236-245	10
α-helix	254-255	2
α-helix	256-259	4
α-helix	271-274	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase CHK1	A	protein	289	HOMO SAPIENS	O14757 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2YDI_1 SERINE/THREONINE-PROTEIN KINASE CHK1 (chains A)
MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICINK
MLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRIEPDIGMPEPDAQRFFHQLMAGVVY
LHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRERLLNKMCGTLPYVAPELLK
RREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLA
LLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSG

Ligands and cofactors

ID	Name	Formula	Copies
YDI	5-[4-(2-dimethylaminoethyloxy)phenyl]-2-ureido-thiophene-3-carboxamide	C16 H20 N4 O3 S	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Discovery of Checkpoint Kinase Inhibitor (S)-5-(3-Fluorophenyl)-N-(Piperidin-3-Yl)-3-Ureidothiophene-2-Carboxamide (Azd7762) by Structure-Based Design and Optimization of Thiophenecarboxamide Ureas. Oza, V., Ashwell, S., Almeida, L. et al. J Med Chem (2012) 55:5130. DOI 10.1021/JM300025R · PubMed

Other PDB entries of the same protein (UniProt O14757 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2YEX 1.3 Å, Synthesis and evaluation of triazolones as checkpoint kinase 1 inhibitors
9CE4 1.31 Å, Structure of CHK1 10-pt. mutant complex with LRRK2 indazole inhibitor compound 6
4HYI 1.4 Å, X-RAY Crystal structure of compound 40 bound to human chk1 kinase domain
3PA3 1.4 Å, X-ray crystal structure of compound 70 bound to human CHK1 kinase domain
5OQ5 1.4 Å, Structure of CHK1 8-pt. mutant complex with aminopyrimido-benzodiazepinone LRRK2 inhibitor
3OT3 1.44 Å, X-ray crystal structure of compound 22k bound to human Chk1 kinase domain
7SUF 1.48 Å, Structure of CHK1 10-pt. mutant complex with LRRK2 inhibitor 06
7SUG 1.48 Å, Structure of CHK1 10-pt. mutant complex with LRRK2 inhibitor 09
8E80 1.49 Å, Structure of LRRK2-CHK1 10-pt. mutant complex with heteroaryl-1H-indazole LRRK2…
5OPB 1.55 Å, Structure of CHK1 10-pt. mutant complex with indazole LRRK2 inhibitor
5OPU 1.55 Å, Structure of CHK1 10-pt. mutant complex with pyrrolopyridine LRRK2 inhibitor
8SIX 1.55 Å, Structure of Compound 13 bound to the CHK1 10-point mutant

Browse structure collections

About this viewer

MolViewer shows 2YDI directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.