6W7O: Ternary complex structure - BTK cIAP compound 17

Ternary complex structure - BTK cIAP compound 17. Determined by X-ray diffraction at 2.17 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 2.17 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,242
Mol. weight: 89.16 kDa
Ligands: TL7, ZN
Released: 18 Nov 2020

Explore 6W7O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W7O contains 46 α-helices and 28 β-strands across 4 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: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	399-401	3
β-strand	406-409	4	1
β-strand	416-420	5	1
β-strand	426-431	6	1
β-strand	437	1	2
α-helix	439-449	11
β-strand	457	1	3
β-strand	460-464	5	1
α-helix	470	1
β-strand	471-475	5	1
β-strand	481	1	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	644-653	10

Chain B: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	399-401	3
β-strand	402-411	10	4
β-strand	414-421	8	4
β-strand	425-432	8	4
β-strand	437	1	5
α-helix	439-449	11
β-strand	457	1	6
β-strand	460-464	5	4
β-strand	470-475	6	4
β-strand	481	1	6
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	6
β-strand	535-537	3	6
α-helix	542-545	4
β-strand	546	1	5
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	616-619	4
α-helix	624-632	9
α-helix	638-640	3
α-helix	644-653	10

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	264-266	3
α-helix	269-274	6
α-helix	275-278	4
α-helix	287-292	6
β-strand	295-297	3	7
β-strand	304-306	3	7
β-strand	312-313	2	7
α-helix	322-329	8
α-helix	334-349	16

Chain D: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	264-266	3
α-helix	269-274	6
α-helix	275-278	4
α-helix	287-292	6
β-strand	295-297	3	8
β-strand	304-306	3	8
β-strand	312-313	2	8
α-helix	322-329	8
α-helix	334-348	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein kinase BTK	A, B	protein	277	Homo sapiens	Q06187 (AlphaFold model)
Baculoviral IAP repeat-containing protein 2	C, D	protein	99	Homo sapiens	Q13490 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6W7O_1 Tyrosine-protein kinase BTK (chains A, B)
SAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEF
IEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMC
KDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVR
WSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLA
SEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES

Sequence of entity 2 (C, D), FASTA

>6W7O_2 Baculoviral IAP repeat-containing protein 2 (chains C, D)
GSGPGSSISNLSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFCCDGGL
RCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRY

Ligands and cofactors

ID	Name	Formula	Copies
TL7	[5-({[(3S)-2-(N-methyl-L-alanyl-3-methyl-L-valyl)-3-{[(1R)-1,2,3,4-tetrahydrona…	C58 H65 F2 N11 O8	2
ZN	Zinc ion	Zn	2

Primary citation

Structural Characterization of BTK:PROTAC:cIAP Ternary Complexes: From Snapshots to Ensembles. Calabrese, M.F., Schiemer, J.S., Horst, R. et al. Nat Chem Biol (2020).

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 6W7O 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.