Zinc in PDB 4ybt: Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{1,3- Dimethyl-2-Oxo-6-[3-(Oxolan-3-Ylmethoxy)Phenoxy]-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1-Methyl-1H-Imidazole-4-Sulfonamide (7L)

The structure of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{1,3- Dimethyl-2-Oxo-6-[3-(Oxolan-3-Ylmethoxy)Phenoxy]-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1-Methyl-1H-Imidazole-4-Sulfonamide (7L), PDB code: 4ybt 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)	33.40 / 1.82
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.656, 36.387, 65.840, 90.00, 111.68, 90.00
R / Rfree (%)	16.7 / 20.9

The binding sites of Zinc atom in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{1,3- Dimethyl-2-Oxo-6-[3-(Oxolan-3-Ylmethoxy)Phenoxy]-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1-Methyl-1H-Imidazole-4-Sulfonamide (7L) (pdb code 4ybt). 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-{1,3- Dimethyl-2-Oxo-6-[3-(Oxolan-3-Ylmethoxy)Phenoxy]-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1-Methyl-1H-Imidazole-4-Sulfonamide (7L), PDB code: 4ybt:
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-{1,3- Dimethyl-2-Oxo-6-[3-(Oxolan-3-Ylmethoxy)Phenoxy]-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1-Methyl-1H-Imidazole-4-Sulfonamide (7L)


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-{1,3- Dimethyl-2-Oxo-6-[3-(Oxolan-3-Ylmethoxy)Phenoxy]-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1-Methyl-1H-Imidazole-4-Sulfonamide (7L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:35.2 occ:1.00 SG A:CYS829 2.2 32.7 1.0 SG A:CYS852 2.3 33.1 1.0 ND1 A:HIS849 2.3 30.3 1.0 SG A:CYS832 2.4 34.9 1.0 CB A:CYS829 3.1 31.9 1.0 CB A:CYS852 3.1 30.0 1.0 CE1 A:HIS849 3.2 38.9 1.0 CG A:HIS849 3.3 34.0 1.0 CB A:CYS832 3.3 32.9 1.0 CB A:HIS849 3.5 32.9 1.0 N A:CYS832 3.8 33.0 1.0 N A:HIS849 4.0 30.6 1.0 CA A:CYS832 4.2 33.6 1.0 NE2 A:HIS849 4.4 35.0 1.0 CA A:HIS849 4.4 33.0 1.0 CD2 A:HIS849 4.4 34.6 1.0 CA A:CYS829 4.5 32.9 1.0 CA A:CYS852 4.6 33.9 1.0 CB A:VAL831 4.6 35.9 1.0 O A:HOH1249 4.7 65.8 1.0 C A:VAL831 4.8 38.1 1.0 C A:CYS832 4.9 33.2 1.0 N A:VAL831 5.0 31.9 1.0 C A:CYS829 5.0 34.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{1,3- Dimethyl-2-Oxo-6-[3-(Oxolan-3-Ylmethoxy)Phenoxy]-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1-Methyl-1H-Imidazole-4-Sulfonamide (7L)


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-{1,3- Dimethyl-2-Oxo-6-[3-(Oxolan-3-Ylmethoxy)Phenoxy]-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1-Methyl-1H-Imidazole-4-Sulfonamide (7L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:34.2 occ:1.00 SG A:CYS844 2.3 33.9 1.0 SG A:CYS870 2.3 33.2 1.0 SG A:CYS841 2.4 32.2 1.0 SG A:CYS867 2.4 31.1 1.0 CB A:CYS841 3.2 33.0 1.0 CB A:CYS844 3.3 35.0 1.0 CB A:CYS870 3.4 29.8 1.0 CB A:CYS867 3.5 28.9 1.0 N A:CYS844 3.8 38.6 1.0 CA A:CYS844 4.1 37.9 1.0 N A:CYS867 4.1 29.6 1.0 N A:CYS870 4.1 26.4 1.0 CA A:CYS867 4.3 28.4 1.0 CA A:CYS870 4.4 31.5 1.0 C A:LYS843 4.6 40.8 1.0 CA A:CYS841 4.7 34.9 1.0 C A:CYS844 4.7 37.9 1.0 O A:CYS867 4.7 25.7 1.0 O A:CYS844 4.7 36.8 1.0 CB A:LYS843 4.7 44.6 1.0 CB A:PHE869 4.8 28.6 1.0 O A:HOH1253 4.8 43.6 1.0 C A:CYS867 4.8 25.2 1.0 N A:LYS843 4.9 38.4 1.0 CA A:LYS843 5.0 38.0 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