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The protac MZ1 in complex with the second bromodomain of BRD4 and PVHL:ELONGINC:ELONGINB

Analyse The protac MZ1 in complex with the second bromodomain of BRD4 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5T35
Type: protein
Length: 901 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 4; Transcription elongation factor B polypeptide 2…
UniProt: O60885, Q15370, Q15369, P40337
Ligands: 759
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 38% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Bromodomain-containing protein 4	protein	111	70% helix, 0% strand	O60885
B, F	Transcription elongation factor B polypeptide 2	protein	104	21% helix, 38% strand	Q15370
C	Transcription elongation factor B polypeptide 1	protein	87	48% helix, 15% strand	Q15369
D	Von hippel-lindau disease tumor suppressor	protein	149	26% helix, 30% strand	P40337
G	Transcription elongation factor B polypeptide 1	protein	88	48% helix, 15% strand	Q15369
H	Von hippel-lindau disease tumor suppressor	protein	147	26% helix, 30% strand	P40337

Ligands and binding sites

759 · (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · 2 copies · chains A, D, E, H

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	651	0.72	0.79	55	759
2	589	0.70	0.78	55	759
3	164	0.49	0.77	27	empty
4	166	0.48	0.77	26	empty
5	115	0.44	0.78	24	empty

Interfaces

10 interfaces between chains.

B–C · 1148 Å² buried · 10 hydrogen bonds · protein-protein
F–G · 1124 Å² buried · 11 hydrogen bonds · protein-protein
G–H · 1085 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1063 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 398 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5T35 · The PROTAC MZ1 in complex with the second bromodomain of Brd4 and pVHL:ElonginC:ElonginB · the same entry in another collection · chain H against H, TM-score 1.00
P40337 · AlphaFold monomer V2.0 prediction for von hippel-lindau disease tumor suppressor (P40337) · a predicted model of the same protein · chain H against A, TM-score 0.99
Q15370 · AlphaFold monomer V2.0 prediction for elongin-B (Q15370) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 O60885
Every structure of UniProt Q15370
Every structure of UniProt Q15369
Every structure of UniProt P40337
Elsewhere: RCSB PDB 5T35 · PDBe 5T35 · UniProt O60885 · UniProt Q15370 · UniProt Q15369 · UniProt P40337

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