5U9D: Tyrosine-protein kinase BTK

Discovery of a potent BTK inhibitor with a novel binding mode using parallel selections with a DNA-encoded chemical library. Determined by X-ray diffraction at 1.33 Å resolution. Released 18 Jan 2017.

Method: X-ray diffraction
Resolution: 1.33 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,842
Mol. weight: 32.48 kDa
Ligands: 83P
Released: 18 Jan 2017

Explore 5U9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5U9D contains 19 α-helices and 12 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: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	396	1	1
α-helix	399-401	3
β-strand	402-411	10	1
β-strand	414-421	8	1
β-strand	425-432	8	1
α-helix	433	1
β-strand	437	1	2
α-helix	439-449	11
β-strand	457	1	3
α-helix	458-459	2
β-strand	460-464	5	1
β-strand	471-474	4	1
β-strand	480-481	2	3
α-helix	482-487	6
α-helix	489-491	3
α-helix	495-514	20
α-helix	524-526	3
β-strand	527-529	3	3
β-strand	535-537	3	3
α-helix	542-545	4
β-strand	546	1	2
α-helix	549-552	4
α-helix	561-563	3
α-helix	566-571	6
α-helix	576-591	16
α-helix	595-596	2
α-helix	603-611	9
α-helix	624-632	9
α-helix	638-640	3
α-helix	642-643	2
α-helix	644-658	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein kinase BTK	A	protein	271	Homo sapiens	Q06187 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5U9D_1 Tyrosine-protein kinase BTK (chains A)
GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKV
MMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEA
MEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEV
LMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYT
IMYSCWHEKADERPTFKILLSNILDVMDEES

Ligands and cofactors

ID	Name	Formula	Copies
83P	(R)-N-methyl-2-(3-((quinoxalin-6-ylamino)methyl)furan-2-carbonyl)-2,3,4,9-tetra…	C27 H24 N6 O3	1

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

Primary citation

Discovery of a Potent BTK Inhibitor with a Novel Binding Mode by Using Parallel Selections with a DNA-Encoded Chemical Library. Cuozzo, J.W., Centrella, P.A., Gikunju, D. et al. Chembiochem (2017) 18:864-871. DOI 10.1002/cbic.201600573 · PubMed

Other PDB entries of the same protein (UniProt Q06187 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5P9J 1.08 Å, BTK1 cocrystallized with ibrutinib
6DI1 1.1 Å, Crystal structure of btk in complex with covalent fragment ligand
5P9I 1.11 Å, BTK1 soaked with ibrutinib-rev
6HRP 1.12 Å, CRYSTAL STRUCTURE OF BTK KINASE DOMAIN COMPLEXED WITH 6-(dimethylamino)-2-[2-(hydroxymeth…
6E4F 1.15 Å, Crystal structure of ARQ 531 in complex with the kinase domain of BTK
4RFZ 1.17 Å, Crystal structure of BTK kinase domain complexed with 6-(dimethylamino)-8-fluoro-2-[2-(hy…
7L5O 1.21 Å, Crystal structure of the noncovalently bonded complex of rilzabrutinib with BTK
5P9L 1.25 Å, BTK1 in complex with cc 292
6DI9 1.25 Å, Crystal structure of btk in complex with covalent inhibitor
6J6M 1.25 Å, Co-crystal structure of BTK kinase domain with Zanubrutinib
7N5O 1.25 Å, Fragment-Based Discovery of a Novel Bruton's Tyrosine Kinase Inhibitor
5P9K 1.28 Å, Crystal structure of btk with cnx 774

Browse structure collections

About this viewer

MolViewer shows 5U9D 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.