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Crystal structure of protac 1 in complex with the bromodomain of human SMARCA2 and PVHL:ELONGINC:ELONGINB

Analyse Crystal structure of protac 1 in complex with the bromodomain of human SMARCA2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HAY
Type: protein
Length: 930 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable global transcription activator SNF2L2; Von hippel-lindau disease tumor…
EC: 3.6.4.-
UniProt: P51531, P40337, Q15369, Q15370
Ligands: FX8
Pockets: 10 · best druggability 0.68

Structure

x-ray diffraction · 8 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable global transcription activator SNF2L2 (EC 3.6.4.-)	protein	120	64% helix, 2% strand	P51531
B	Von hippel-lindau disease tumor suppressor	protein	152	26% helix, 28% strand	P40337
C	Elongin-C	protein	97	41% helix, 13% strand	Q15369
D	Elongin-B	protein	104	21% helix, 38% strand	Q15370
E	Probable global transcription activator SNF2L2 (EC 3.6.4.-)	protein	115	64% helix, 2% strand	P51531
F	Von hippel-lindau disease tumor suppressor	protein	151	26% helix, 28% strand	P40337
G	Elongin-C	protein	88	48% helix, 15% strand	Q15369
H	Elongin-B	protein	103	15% helix, 39% strand	Q15370

Ligands and binding sites

FX8 · (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]ethoxy]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · 2 copies · chains A, B, E, F
EDO · 1,2-ethanediol · additive · 22 copies · chains B, C, A, D, F, G, E, H
FMT · Formic acid · additive · chains B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	430	0.68	0.80	46	FX8, EDO
2	432	0.66	0.78	42	FX8, EDO
3	228	0.57	0.79	49	empty
4	84	0.53	0.85	24	empty
5	230	0.48	0.74	35	EDO

Interfaces

12 interfaces between chains.

C–D · 1145 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 1142 Å² buried · 14 hydrogen bonds · protein-protein
F–G · 1109 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1092 Å² buried · 14 hydrogen bonds · protein-protein
B–F · 823 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6HAY · Crystal structure of PROTAC 1 in complex with the bromodomain of human SMARCA2 and… · the same entry in another collection · chain H against H, TM-score 1.00
Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · a predicted model of the same protein · chain H against A, TM-score 0.99
Q15369 · AlphaFold monomer V2.0 prediction for elongin-C (Q15369) · a predicted model of the same protein · chain G against A, TM-score 0.98
P51531 · AlphaFold monomer V2.0 prediction for probable global transcription activator SNF2L2… · a predicted model of the same protein · chain E against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P51531
Every structure of UniProt P40337
Every structure of UniProt Q15369
Every structure of UniProt Q15370
Elsewhere: RCSB PDB 6HAY · PDBe 6HAY · UniProt P51531 · UniProt P40337 · UniProt Q15369 · UniProt Q15370

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