Sodium in PDB 7mlr: X-Ray Crystal Structure of Human BRD4(D1) in Complex with 2-(4-{5-[6- (3,5-Dimethylphenoxy)Pyridin-2-Yl]-4-Methyl-1H-1,2,3-Triazol-1- Yl}Piperidin-1-Yl)-N,N-Dimethylethan-1-Amine (DW34)

Protein crystallography data

The structure of X-Ray Crystal Structure of Human BRD4(D1) in Complex with 2-(4-{5-[6- (3,5-Dimethylphenoxy)Pyridin-2-Yl]-4-Methyl-1H-1,2,3-Triazol-1- Yl}Piperidin-1-Yl)-N,N-Dimethylethan-1-Amine (DW34), PDB code: 7mlr was solved by H.Cui, K.Shi, H.Aihara, W.C.K.Pomerantz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.66 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.098, 44.336, 78.936, 90, 90, 90
R / Rfree (%) 13.6 / 16.4

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystal Structure of Human BRD4(D1) in Complex with 2-(4-{5-[6- (3,5-Dimethylphenoxy)Pyridin-2-Yl]-4-Methyl-1H-1,2,3-Triazol-1- Yl}Piperidin-1-Yl)-N,N-Dimethylethan-1-Amine (DW34) (pdb code 7mlr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Crystal Structure of Human BRD4(D1) in Complex with 2-(4-{5-[6- (3,5-Dimethylphenoxy)Pyridin-2-Yl]-4-Methyl-1H-1,2,3-Triazol-1- Yl}Piperidin-1-Yl)-N,N-Dimethylethan-1-Amine (DW34), PDB code: 7mlr:

Sodium binding site 1 out of 1 in 7mlr

Go back to Sodium Binding Sites List in 7mlr
Sodium binding site 1 out of 1 in the X-Ray Crystal Structure of Human BRD4(D1) in Complex with 2-(4-{5-[6- (3,5-Dimethylphenoxy)Pyridin-2-Yl]-4-Methyl-1H-1,2,3-Triazol-1- Yl}Piperidin-1-Yl)-N,N-Dimethylethan-1-Amine (DW34)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Human BRD4(D1) in Complex with 2-(4-{5-[6- (3,5-Dimethylphenoxy)Pyridin-2-Yl]-4-Methyl-1H-1,2,3-Triazol-1- Yl}Piperidin-1-Yl)-N,N-Dimethylethan-1-Amine (DW34) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:49.0
occ:1.00
HZ1 A:LYS55 2.1 22.8 1.0
OE1 A:GLU124 2.2 21.8 1.0
O A:HOH461 2.3 28.5 1.0
CD A:GLU124 2.5 24.4 1.0
HE3 A:LYS55 2.6 26.2 1.0
NZ A:LYS55 2.8 19.0 1.0
HB3 A:GLU124 2.9 20.0 1.0
CE A:LYS55 2.9 21.8 1.0
HD1 A:TYR119 3.0 17.1 1.0
HE2 A:LYS55 3.0 26.2 1.0
OE2 A:GLU124 3.0 25.7 1.0
HZ2 A:LYS55 3.1 22.8 1.0
CG A:GLU124 3.3 21.0 1.0
HA A:TYR119 3.4 15.8 1.0
HG2 A:GLU124 3.4 25.2 1.0
HZ3 A:LYS55 3.5 22.8 1.0
CB A:GLU124 3.5 16.7 1.0
HE2 A:TYR118 3.6 17.4 1.0
H A:TRP120 3.7 17.4 1.0
HB2 A:GLU124 3.8 20.0 1.0
CD1 A:TYR119 3.8 14.2 1.0
O A:HOH369 4.0 30.8 1.0
CE2 A:TYR118 4.2 14.5 1.0
HD2 A:TYR118 4.2 17.8 1.0
HG3 A:GLU124 4.2 25.2 1.0
CA A:TYR119 4.3 13.2 1.0
O A:HOH342 4.3 38.0 1.0
HE1 A:TYR119 4.4 16.3 1.0
CD A:LYS55 4.4 21.5 1.0
CD2 A:TYR118 4.5 14.8 1.0
O A:HOH347 4.5 23.4 1.0
O A:HOH450 4.5 46.2 1.0
N A:TRP120 4.5 14.5 1.0
O A:TYR118 4.5 14.1 1.0
HB3 A:TYR119 4.6 15.7 1.0
CE1 A:TYR119 4.6 13.6 1.0
HD3 A:LYS55 4.7 25.8 1.0
CG A:TYR119 4.7 13.2 1.0
CB A:TYR119 4.8 13.1 1.0
HD2 A:LYS55 4.8 25.8 1.0
CA A:GLU124 4.9 14.3 1.0
O A:HOH304 4.9 34.8 1.0
O A:HOH483 4.9 44.3 1.0
C A:TYR119 5.0 13.4 1.0

Reference:

H.Cui, A.S.Carlson, M.A.Schleiff, A.Divakaran, J.A.Johnson, C.R.Buchholz, H.Zahid, N.R.Vail, K.Shi, H.Aihara, D.A.Harki, G.P.Miller, J.J.Topczewski, W.C.K.Pomerantz. 4-Methyl-1,2,3-Triazoles As N -Acetyl-Lysine Mimics Afford Potent Bet Bromodomain Inhibitors with Improved Selectivity. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34236185
DOI: 10.1021/ACS.JMEDCHEM.1C00933
Page generated: Sat Aug 21 17:23:57 2021

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