Bromine in PDB 8uqh: X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130

The structure of X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130, PDB code: 8uqh was solved by M.Bush, N.Noinaj, Y.Deng, R.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.71 / 1.87
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.726, 98.728, 206.118, 90, 90, 90
R / Rfree (%)	21.4 / 25.3

The binding sites of Bromine atom in the X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130 (pdb code 8uqh). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130, PDB code: 8uqh:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in the X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br501 b:44.9 occ:0.66 BR23 A:X9L501 0.0 44.9 0.7 C22 A:X9L501 1.9 33.1 0.7 C25 A:X9L501 2.0 32.9 0.3 C26 A:X9L501 2.8 31.7 0.3 C24 A:X9L501 2.9 30.8 0.7 C21 A:X9L501 2.9 32.2 0.7 C24 A:X9L501 3.0 31.6 0.3 CB A:HIS415 3.6 30.2 1.0 CH2 A:TRP416 3.7 26.9 1.0 CD A:ARG169 3.8 31.1 1.0 CZ3 A:TRP416 3.8 24.4 1.0 CZ2 A:TRP416 3.9 31.9 1.0 CE3 A:TRP416 4.0 23.3 1.0 CE2 A:TRP416 4.0 25.7 1.0 CD2 A:TRP416 4.1 25.8 1.0 C20 A:X9L501 4.1 34.9 0.3 OD2 A:ASP166 4.1 37.3 1.0 C25 A:X9L501 4.2 34.5 0.7 C20 A:X9L501 4.2 35.7 0.7 C22 A:X9L501 4.3 34.6 0.3 CG A:MET163 4.3 36.0 1.0 NE A:ARG169 4.4 34.5 1.0 CG A:HIS415 4.4 47.9 1.0 CG A:ASP166 4.4 33.6 1.0 CB A:ASP166 4.5 34.8 1.0 CA A:HIS415 4.5 28.9 1.0 CD2 A:HIS415 4.5 48.0 1.0 CA A:MET163 4.5 34.3 1.0 N A:HIS415 4.6 25.1 1.0 CB A:MET163 4.6 34.3 1.0 C A:HIS415 4.6 30.6 1.0 N A:TRP416 4.7 25.8 1.0 C26 A:X9L501 4.7 34.6 0.7 C21 A:X9L501 4.7 34.7 0.3 CB A:ARG169 4.8 30.6 1.0 NE1 A:TRP416 4.8 31.2 1.0 O A:MET163 4.8 32.7 1.0 CG A:ARG169 4.9 30.4 1.0 CG A:TRP416 4.9 27.9 1.0

Bromine binding site 2 out of 8 in the X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br501 b:68.2 occ:0.34 BR23 A:X9L501 0.0 68.2 0.3 C25 A:X9L501 1.8 34.5 0.7 C22 A:X9L501 1.9 34.6 0.3 C26 A:X9L501 2.3 34.6 0.7 C21 A:X9L501 2.8 34.7 0.3 C24 A:X9L501 2.9 31.6 0.3 C24 A:X9L501 3.1 30.8 0.7 O A:HOH609 3.2 27.7 1.0 CE1 A:TYR262 3.2 36.4 1.0 CZ A:TYR262 3.3 40.9 1.0 CD1 A:TYR262 3.5 32.9 1.0 CE2 A:TYR262 3.5 35.8 1.0 O A:HOH839 3.7 43.3 1.0 C20 A:X9L501 3.7 35.7 0.7 CG A:TYR262 3.7 31.1 1.0 CD2 A:TYR262 3.7 32.7 1.0 OH A:TYR262 3.8 42.2 1.0 CD1 A:TRP416 4.0 26.9 1.0 O A:HIS415 4.0 27.5 1.0 O A:HOH614 4.0 42.0 1.0 N A:TYR262 4.0 27.5 1.0 C20 A:X9L501 4.1 34.9 0.3 C25 A:X9L501 4.2 32.9 0.3 C22 A:X9L501 4.2 33.1 0.7 OE2 A:GLU267 4.3 34.7 1.0 NE1 A:TRP416 4.4 31.2 1.0 C21 A:X9L501 4.5 32.2 0.7 CA A:TRP416 4.6 23.9 1.0 C A:GLY261 4.6 24.0 1.0 CA A:TYR262 4.7 27.5 1.0 C26 A:X9L501 4.7 31.7 0.3 CA A:GLY261 4.7 26.7 1.0 CG A:TRP416 4.7 27.9 1.0 CB A:TYR262 4.7 28.2 1.0 C19 A:X9L501 4.8 35.2 0.7 C A:HIS415 4.8 30.6 1.0 O A:HOH681 4.9 37.5 1.0

Bromine binding site 3 out of 8 in the X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br501 b:33.1 occ:0.72 BR23 B:X9L501 0.0 33.1 0.7 C25 B:X9L501 1.9 30.7 0.3 C22 B:X9L501 1.9 30.8 0.7 C26 B:X9L501 2.6 29.3 0.3 C21 B:X9L501 2.9 28.8 0.7 C24 B:X9L501 2.9 30.8 0.7 C24 B:X9L501 3.0 30.6 0.3 CB B:HIS415 3.7 34.7 1.0 OD2 B:ASP166 3.8 32.6 1.0 CD B:ARG169 3.8 24.9 1.0 CH2 B:TRP416 3.9 19.6 1.0 CZ2 B:TRP416 3.9 25.6 1.0 C20 B:X9L501 4.0 30.9 0.3 CZ3 B:TRP416 4.0 21.2 1.0 CE2 B:TRP416 4.0 25.5 1.0 CD2 B:TRP416 4.1 24.5 1.0 CE3 B:TRP416 4.1 23.9 1.0 C20 B:X9L501 4.2 31.0 0.7 C22 B:X9L501 4.2 31.6 0.3 C25 B:X9L501 4.2 30.5 0.7 NE B:ARG169 4.4 20.9 1.0 CG B:MET163 4.4 29.4 1.0 CA B:HIS415 4.5 29.7 1.0 CB B:ASP166 4.5 30.9 1.0 CG B:ASP166 4.5 31.9 1.0 C B:HIS415 4.5 26.7 1.0 N B:HIS415 4.5 25.4 1.0 C21 B:X9L501 4.6 31.0 0.3 CA B:MET163 4.6 26.9 1.0 N B:TRP416 4.6 26.4 1.0 ND1 B:HIS415 4.6 50.0 1.0 CG B:HIS415 4.6 45.1 1.0 NE1 B:TRP416 4.7 25.7 1.0 CB B:MET163 4.7 25.4 1.0 C26 B:X9L501 4.7 30.8 0.7 CG B:TRP416 4.8 24.0 1.0 CB B:ARG169 4.8 18.4 1.0 O B:MET163 4.9 27.7 1.0 CG B:ARG169 4.9 23.6 1.0 OE2 B:GLU258 4.9 24.4 1.0

Bromine binding site 4 out of 8 in the X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br501 b:82.3 occ:0.28 BR23 B:X9L501 0.0 82.3 0.3 C25 B:X9L501 1.7 30.5 0.7 C22 B:X9L501 1.9 31.6 0.3 C26 B:X9L501 2.1 30.8 0.7 C21 B:X9L501 2.8 31.0 0.3 C24 B:X9L501 2.9 30.6 0.3 C24 B:X9L501 3.0 30.8 0.7 O B:HOH646 3.2 20.1 1.0 CE1 B:TYR262 3.2 34.3 1.0 CZ B:TYR262 3.3 34.3 1.0 CD1 B:TYR262 3.4 32.8 1.0 CE2 B:TYR262 3.4 38.6 1.0 C20 B:X9L501 3.5 31.0 0.7 CG B:TYR262 3.5 30.8 1.0 CD2 B:TYR262 3.6 34.2 1.0 CD1 B:TRP416 3.8 23.5 1.0 N B:TYR262 3.8 25.8 1.0 OH B:TYR262 3.9 41.1 1.0 C22 B:X9L501 4.1 30.8 0.7 C20 B:X9L501 4.1 30.9 0.3 O B:HOH602 4.2 34.8 1.0 O B:HIS415 4.2 22.6 1.0 O B:HOH814 4.2 53.2 1.0 C25 B:X9L501 4.2 30.7 0.3 NE1 B:TRP416 4.3 25.7 1.0 C21 B:X9L501 4.3 28.8 0.7 C B:GLY261 4.3 22.9 1.0 CA B:TYR262 4.4 27.1 1.0 OE2 B:GLU267 4.4 37.7 1.0 O B:HOH798 4.5 45.4 1.0 CA B:GLY261 4.5 21.4 1.0 CB B:TYR262 4.5 27.1 1.0 C19 B:X9L501 4.6 32.1 0.7 CA B:TRP416 4.6 30.1 1.0 CG B:TRP416 4.6 24.0 1.0 C26 B:X9L501 4.7 29.3 0.3 C B:HIS415 5.0 26.7 1.0

Bromine binding site 5 out of 8 in the X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br501 b:44.0 occ:0.71 BR23 C:X9L501 0.0 44.0 0.7 C22 C:X9L501 1.9 39.6 0.7 C25 C:X9L501 2.0 39.4 0.3 C26 C:X9L501 2.5 38.3 0.3 C24 C:X9L501 2.9 38.0 0.7 C21 C:X9L501 2.9 38.7 0.7 C24 C:X9L501 3.2 38.2 0.3 CB C:HIS415 3.5 41.7 1.0 C20 C:X9L501 3.8 38.3 0.3 CD C:ARG169 4.1 36.7 1.0 OD2 C:ASP166 4.2 36.3 1.0 CZ3 C:TRP416 4.2 32.1 1.0 C20 C:X9L501 4.2 38.4 0.7 C25 C:X9L501 4.2 38.4 0.7 CH2 C:TRP416 4.2 29.4 1.0 CE3 C:TRP416 4.2 33.6 1.0 CD2 C:TRP416 4.3 32.4 1.0 CZ2 C:TRP416 4.3 28.1 1.0 CE2 C:TRP416 4.3 29.7 1.0 C22 C:X9L501 4.4 39.6 0.3 CA C:HIS415 4.4 36.8 1.0 CA C:MET163 4.5 31.1 1.0 CB C:MET163 4.5 28.7 1.0 CG C:HIS415 4.5 51.6 1.0 C C:HIS415 4.5 30.8 1.0 CG C:MET163 4.5 28.2 1.0 CB C:ASP166 4.6 29.9 1.0 N C:HIS415 4.6 25.7 1.0 C21 C:X9L501 4.6 38.7 0.3 N C:TRP416 4.6 27.4 1.0 CG C:ASP166 4.6 35.2 1.0 O C:MET163 4.7 26.3 1.0 C26 C:X9L501 4.7 39.0 0.7 OE2 C:GLU258 4.7 39.7 1.0 ND1 C:HIS415 4.7 52.5 1.0 CG C:ARG169 4.8 34.7 1.0 C19 C:X9L501 4.9 38.5 0.3 CB C:ARG169 4.9 33.2 1.0 O C:HOH802 4.9 46.3 1.0 NE1 C:TRP416 5.0 30.2 1.0 CG C:TRP416 5.0 29.6 1.0

Bromine binding site 6 out of 8 in the X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130 within 5.0Å range: probe atom residue distance (Å) B Occ C:Br501 b:78.2 occ:0.29 BR23 C:X9L501 0.0 78.2 0.3 C25 C:X9L501 1.9 38.4 0.7 C22 C:X9L501 1.9 39.6 0.3 C26 C:X9L501 2.0 39.0 0.7 C21 C:X9L501 2.8 38.7 0.3 C24 C:X9L501 2.9 38.2 0.3 O C:HOH621 2.9 33.5 1.0 CZ C:TYR262 3.2 49.7 1.0 CE1 C:TYR262 3.3 38.4 1.0 C24 C:X9L501 3.3 38.0 0.7 CE2 C:TYR262 3.3 44.2 1.0 C20 C:X9L501 3.4 38.4 0.7 CD1 C:TYR262 3.4 44.2 1.0 CD2 C:TYR262 3.5 40.0 1.0 CG C:TYR262 3.6 39.2 1.0 O C:HOH814 3.7 44.5 1.0 N C:TYR262 3.8 32.4 1.0 OH C:TYR262 3.9 48.4 1.0 OE2 C:GLU267 4.1 40.9 1.0 C20 C:X9L501 4.2 38.3 0.3 C25 C:X9L501 4.2 39.4 0.3 CD1 C:TRP416 4.2 32.0 1.0 C19 C:X9L501 4.2 37.8 0.7 C22 C:X9L501 4.3 39.6 0.7 C C:GLY261 4.3 28.3 1.0 C21 C:X9L501 4.3 38.7 0.7 CA C:GLY261 4.4 35.2 1.0 CB C:TYR262 4.5 33.6 1.0 CA C:TYR262 4.5 37.4 1.0 NE1 C:TRP416 4.5 30.2 1.0 O C:HOH637 4.6 42.1 1.0 C26 C:X9L501 4.7 38.3 0.3 O C:HIS415 4.9 32.8 1.0

Bromine binding site 7 out of 8 in the X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130 within 5.0Å range: probe atom residue distance (Å) B Occ D:Br501 b:45.7 occ:0.70 BR23 D:X9L501 0.0 45.7 0.7 C22 D:X9L501 1.9 36.1 0.7 C25 D:X9L501 2.1 36.0 0.3 C26 D:X9L501 2.7 34.3 0.3 C24 D:X9L501 2.9 34.5 0.7 C21 D:X9L501 2.9 34.0 0.7 C24 D:X9L501 3.4 35.3 0.3 CB D:HIS415 3.5 45.7 1.0 CZ3 D:TRP416 3.9 30.7 1.0 CH2 D:TRP416 3.9 27.2 1.0 OD2 D:ASP166 3.9 35.0 1.0 CE3 D:TRP416 4.0 28.7 1.0 CZ2 D:TRP416 4.0 33.2 1.0 C20 D:X9L501 4.0 34.8 0.3 CE2 D:TRP416 4.1 31.7 1.0 CD2 D:TRP416 4.1 32.0 1.0 C20 D:X9L501 4.2 35.4 0.7 C25 D:X9L501 4.2 34.8 0.7 CA D:HIS415 4.4 40.1 1.0 CB D:ASP166 4.5 23.5 1.0 CG D:ASP166 4.5 37.2 1.0 CG D:MET163 4.5 24.0 1.0 C D:HIS415 4.5 36.5 1.0 CD D:ARG169 4.5 36.6 1.0 C22 D:X9L501 4.5 36.1 0.3 N D:HIS415 4.5 41.3 1.0 N D:TRP416 4.5 31.9 1.0 NE D:ARG169 4.6 39.8 1.0 CG D:HIS415 4.6 55.8 1.0 ND1 D:HIS415 4.6 53.2 1.0 CA D:MET163 4.7 20.1 1.0 C26 D:X9L501 4.7 35.0 0.7 CB D:MET163 4.7 25.7 1.0 NE1 D:TRP416 4.8 34.1 1.0 C21 D:X9L501 4.8 35.6 0.3 CG D:TRP416 4.8 29.0 1.0 O D:MET163 4.8 30.2 1.0 CB D:ARG169 4.9 33.0 1.0 CG D:ARG169 4.9 35.1 1.0

Bromine binding site 8 out of 8 in the X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of X-Ray Crystal Structure of PRMT4 Bound to Compound Yd-1130 within 5.0Å range: probe atom residue distance (Å) B Occ D:Br501 b:76.8 occ:0.30 BR23 D:X9L501 0.0 76.8 0.3 C22 D:X9L501 1.9 36.1 0.3 C25 D:X9L501 2.1 34.8 0.7 C26 D:X9L501 2.2 35.0 0.7 C21 D:X9L501 2.9 35.6 0.3 C24 D:X9L501 2.9 35.3 0.3 O D:HOH661 3.1 34.5 1.0 CZ D:TYR262 3.3 47.0 1.0 CE1 D:TYR262 3.3 40.6 1.0 CE2 D:TYR262 3.4 42.1 1.0 C24 D:X9L501 3.4 34.5 0.7 CD1 D:TYR262 3.5 39.5 1.0 C20 D:X9L501 3.6 35.4 0.7 CD2 D:TYR262 3.6 41.5 1.0 CG D:TYR262 3.6 37.5 1.0 OH D:TYR262 3.9 52.8 1.0 N D:TYR262 3.9 29.2 1.0 C20 D:X9L501 4.2 34.8 0.3 OE2 D:GLU267 4.2 41.8 1.0 C25 D:X9L501 4.2 36.0 0.3 O D:HOH608 4.3 40.5 1.0 CD1 D:TRP416 4.4 29.0 1.0 C22 D:X9L501 4.4 36.1 0.7 C19 D:X9L501 4.4 34.1 0.7 C21 D:X9L501 4.5 34.0 0.7 C D:GLY261 4.5 30.9 1.0 CA D:GLY261 4.6 31.1 1.0 CB D:TYR262 4.6 33.7 1.0 CA D:TYR262 4.7 32.7 1.0 C26 D:X9L501 4.7 34.3 0.3 NE1 D:TRP416 4.8 34.1 1.0 O D:HIS415 4.8 33.2 1.0

Y.Deng, E.J.Kim, X.Song, A.S.Kulkarni, R.X.Zhu, Y.Wang, M.Bush, A.Dong, N.Noinaj, J.Min, W.Xu, R.Huang. An Adenosine Analogue Library Reveals Insights Into Active Sites of Protein Arginine Methyltransferases and Enables the Discovery of A Selective PRMT4 Inhibitor. J.Med.Chem. V. 67 18053 2024.
ISSN: ISSN 0022-2623
PubMed: 39361813
DOI: 10.1021/ACS.JMEDCHEM.4C01041