Zinc in PDB 4yc9: Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(6-{3-[4- (Dimethylamino)Butoxy]-5-Propoxyphenoxy}-1,3-Dimethyl-2-Oxo-2,3- Dihydro-1H-1,3-Benzodiazol-5-Yl)-3,4-Dimethoxybenzene-1-Sulfonamide (8I)

The structure of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(6-{3-[4- (Dimethylamino)Butoxy]-5-Propoxyphenoxy}-1,3-Dimethyl-2-Oxo-2,3- Dihydro-1H-1,3-Benzodiazol-5-Yl)-3,4-Dimethoxybenzene-1-Sulfonamide (8I), PDB code: 4yc9 was solved by G.Poncet-Montange, W.Palmer, P.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.58 / 1.82
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.839, 35.624, 65.367, 90.00, 112.07, 90.00
R / Rfree (%)	15.5 / 20.4

The binding sites of Zinc atom in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(6-{3-[4- (Dimethylamino)Butoxy]-5-Propoxyphenoxy}-1,3-Dimethyl-2-Oxo-2,3- Dihydro-1H-1,3-Benzodiazol-5-Yl)-3,4-Dimethoxybenzene-1-Sulfonamide (8I) (pdb code 4yc9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(6-{3-[4- (Dimethylamino)Butoxy]-5-Propoxyphenoxy}-1,3-Dimethyl-2-Oxo-2,3- Dihydro-1H-1,3-Benzodiazol-5-Yl)-3,4-Dimethoxybenzene-1-Sulfonamide (8I), PDB code: 4yc9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(6-{3-[4- (Dimethylamino)Butoxy]-5-Propoxyphenoxy}-1,3-Dimethyl-2-Oxo-2,3- Dihydro-1H-1,3-Benzodiazol-5-Yl)-3,4-Dimethoxybenzene-1-Sulfonamide (8I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(6-{3-[4- (Dimethylamino)Butoxy]-5-Propoxyphenoxy}-1,3-Dimethyl-2-Oxo-2,3- Dihydro-1H-1,3-Benzodiazol-5-Yl)-3,4-Dimethoxybenzene-1-Sulfonamide (8I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:28.7 occ:1.00 ND1 A:HIS849 2.2 26.5 1.0 SG A:CYS829 2.3 26.6 1.0 SG A:CYS852 2.3 26.2 1.0 SG A:CYS832 2.4 28.8 1.0 CE1 A:HIS849 3.1 29.4 1.0 CB A:CYS852 3.1 25.0 1.0 CB A:CYS829 3.2 24.2 1.0 CG A:HIS849 3.2 29.9 1.0 CB A:CYS832 3.3 29.8 1.0 CB A:HIS849 3.6 28.1 1.0 N A:CYS832 3.8 25.4 1.0 N A:HIS849 4.0 22.5 1.0 CA A:CYS832 4.1 27.2 1.0 NE2 A:HIS849 4.2 28.6 1.0 CD2 A:HIS849 4.3 29.1 1.0 CA A:HIS849 4.4 25.2 1.0 CB A:VAL831 4.5 27.1 1.0 CA A:CYS829 4.6 25.2 1.0 CA A:CYS852 4.6 25.3 1.0 O A:HOH1330 4.6 40.5 1.0 O A:HOH1275 4.8 52.2 1.0 C A:VAL831 4.8 32.1 1.0 C A:CYS832 4.9 33.5 1.0 CG1 A:VAL831 5.0 28.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(6-{3-[4- (Dimethylamino)Butoxy]-5-Propoxyphenoxy}-1,3-Dimethyl-2-Oxo-2,3- Dihydro-1H-1,3-Benzodiazol-5-Yl)-3,4-Dimethoxybenzene-1-Sulfonamide (8I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(6-{3-[4- (Dimethylamino)Butoxy]-5-Propoxyphenoxy}-1,3-Dimethyl-2-Oxo-2,3- Dihydro-1H-1,3-Benzodiazol-5-Yl)-3,4-Dimethoxybenzene-1-Sulfonamide (8I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:26.6 occ:1.00 SG A:CYS870 2.3 27.0 1.0 SG A:CYS841 2.4 26.1 1.0 SG A:CYS844 2.4 25.6 1.0 SG A:CYS867 2.4 24.5 1.0 CB A:CYS841 3.2 24.3 1.0 CB A:CYS844 3.3 31.2 1.0 CB A:CYS870 3.3 24.9 1.0 CB A:CYS867 3.6 23.4 1.0 N A:CYS844 3.9 30.7 1.0 N A:CYS867 4.0 24.4 1.0 N A:CYS870 4.1 22.4 1.0 CA A:CYS844 4.1 30.8 1.0 CA A:CYS867 4.3 22.9 1.0 CA A:CYS870 4.3 23.1 1.0 C A:LYS843 4.5 30.5 1.0 O A:HOH1240 4.6 58.8 1.0 CA A:CYS841 4.7 25.4 1.0 C A:CYS844 4.7 30.4 1.0 O A:CYS867 4.7 22.9 1.0 C A:CYS867 4.7 21.9 1.0 CB A:PHE869 4.7 24.4 1.0 CB A:LYS843 4.7 34.9 1.0 O A:CYS844 4.8 27.4 1.0 N A:LYS843 4.9 27.4 1.0 CA A:LYS843 5.0 30.3 1.0 C A:PHE869 5.0 24.9 1.0

W.S.Palmer, G.Poncet-Montange, G.Liu, A.Petrocchi, N.Reyna, G.Subramanian, J.Theroff, A.Yau, M.Kost-Alimova, J.P.Bardenhagen, E.Leo, H.E.Shepard, T.N.Tieu, X.Shi, Y.Zhan, S.Zhao, M.C.Barton, G.Draetta, C.Toniatti, P.Jones, M.Geck Do, J.N.Andersen. Structure-Guided Design of Iacs-9571, A Selective High-Affinity Dual TRIM24-BRPF1 Bromodomain Inhibitor. J.Med.Chem. V. 59 1440 2016.
ISSN: ISSN 0022-2623
PubMed: 26061247
DOI: 10.1021/ACS.JMEDCHEM.5B00405