Zinc in PDB 4ybm: Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{6-[3- (Benzyloxy)Phenoxy]-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-3,4-Dimethoxybenzene-1-Sulfonamide (7B)

The structure of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{6-[3- (Benzyloxy)Phenoxy]-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-3,4-Dimethoxybenzene-1-Sulfonamide (7B), PDB code: 4ybm 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)	33.87 / 1.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.400, 79.820, 131.690, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.6

The binding sites of Zinc atom in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{6-[3- (Benzyloxy)Phenoxy]-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-3,4-Dimethoxybenzene-1-Sulfonamide (7B) (pdb code 4ybm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{6-[3- (Benzyloxy)Phenoxy]-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-3,4-Dimethoxybenzene-1-Sulfonamide (7B), PDB code: 4ybm:
Jump to Zinc binding site number: 1; 2; 3; 4;

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


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- (Benzyloxy)Phenoxy]-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-3,4-Dimethoxybenzene-1-Sulfonamide (7B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:17.8 occ:1.00 ND1 A:HIS849 2.0 14.1 1.0 SG A:CYS852 2.3 18.8 1.0 SG A:CYS832 2.3 19.6 1.0 SG A:CYS829 2.4 17.9 1.0 CE1 A:HIS849 2.9 20.6 1.0 CB A:CYS829 3.1 16.2 1.0 CG A:HIS849 3.1 15.7 1.0 CB A:CYS852 3.2 19.3 1.0 CB A:CYS832 3.3 19.2 1.0 CB A:HIS849 3.5 15.9 1.0 N A:CYS832 3.8 19.5 1.0 NE2 A:HIS849 4.0 20.1 1.0 N A:HIS849 4.1 15.9 1.0 CA A:CYS832 4.1 19.3 1.0 CD2 A:HIS849 4.1 19.7 1.0 O A:HOH1473 4.3 55.5 1.0 CA A:HIS849 4.4 15.6 1.0 CA A:CYS829 4.5 17.2 1.0 CA A:CYS852 4.6 15.7 1.0 CB A:VAL831 4.8 17.8 1.0 C A:CYS832 4.9 17.2 1.0 C A:VAL831 5.0 18.6 1.0 N A:GLN833 5.0 18.9 1.0

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


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- (Benzyloxy)Phenoxy]-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-3,4-Dimethoxybenzene-1-Sulfonamide (7B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:20.1 occ:1.00 SG A:CYS870 2.3 21.4 1.0 SG A:CYS841 2.3 21.9 1.0 SG A:CYS867 2.4 19.3 1.0 SG A:CYS844 2.4 22.6 1.0 CB A:CYS841 3.2 19.7 1.0 CB A:CYS870 3.3 20.8 1.0 CB A:CYS844 3.3 23.5 1.0 CB A:CYS867 3.5 19.4 1.0 N A:CYS844 3.8 22.0 1.0 N A:CYS867 4.0 19.2 1.0 CA A:CYS844 4.0 20.8 1.0 N A:CYS870 4.2 17.7 1.0 CA A:CYS867 4.2 17.2 1.0 O A:HOH1313 4.3 32.6 1.0 CA A:CYS870 4.3 18.2 1.0 C A:LYS843 4.5 24.4 1.0 C A:CYS844 4.7 21.7 1.0 CA A:CYS841 4.7 19.9 1.0 C A:CYS867 4.7 16.9 1.0 O A:CYS867 4.7 18.1 1.0 CB A:PHE869 4.8 17.3 1.0 CB A:LYS843 4.8 31.0 1.0 O A:HOH1317 4.8 33.1 1.0 O A:CYS844 4.8 24.4 1.0 N A:LYS843 4.9 24.9 1.0 CA A:LYS843 4.9 27.7 1.0 CG2 A:ILE866 5.0 26.7 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{6-[3- (Benzyloxy)Phenoxy]-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-3,4-Dimethoxybenzene-1-Sulfonamide (7B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1104 b:19.4 occ:1.00 ND1 B:HIS849 2.1 16.6 1.0 SG B:CYS852 2.3 19.6 1.0 SG B:CYS832 2.3 22.2 1.0 SG B:CYS829 2.4 20.0 1.0 CB B:CYS829 3.0 19.7 1.0 CE1 B:HIS849 3.1 21.9 1.0 CG B:HIS849 3.2 17.6 1.0 CB B:CYS852 3.2 18.3 1.0 CB B:CYS832 3.4 22.2 1.0 CB B:HIS849 3.6 16.6 1.0 N B:CYS832 3.8 21.1 1.0 N B:HIS849 4.0 17.4 1.0 CA B:CYS832 4.1 22.3 1.0 NE2 B:HIS849 4.2 21.2 1.0 CD2 B:HIS849 4.3 21.1 1.0 CA B:HIS849 4.4 16.1 1.0 CA B:CYS829 4.5 19.7 1.0 O B:HOH1430 4.5 47.3 1.0 CA B:CYS852 4.6 16.2 1.0 CB B:VAL831 4.8 20.9 1.0 O B:HOH1338 4.9 36.9 1.0 C B:CYS832 4.9 22.1 1.0 C B:VAL831 4.9 23.5 1.0 N B:GLN833 5.0 23.9 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{6-[3- (Benzyloxy)Phenoxy]-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-3,4-Dimethoxybenzene-1-Sulfonamide (7B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1105 b:25.9 occ:1.00 SG B:CYS867 2.3 24.1 1.0 SG B:CYS841 2.3 27.4 1.0 SG B:CYS870 2.3 29.3 1.0 SG B:CYS844 2.4 29.1 1.0 CB B:CYS841 3.2 27.1 1.0 CB B:CYS870 3.3 24.5 1.0 CB B:CYS844 3.4 29.0 1.0 CB B:CYS867 3.4 21.2 1.0 N B:CYS844 3.8 31.6 1.0 N B:CYS867 3.9 24.8 1.0 N B:CYS870 4.1 24.0 1.0 CA B:CYS844 4.1 29.4 1.0 CA B:CYS867 4.2 22.3 1.0 CA B:CYS870 4.3 25.1 1.0 O B:HOH1376 4.5 44.6 1.0 O B:HOH1349 4.5 37.5 1.0 C B:CYS867 4.6 22.5 1.0 C B:LYS843 4.7 39.8 1.0 CA B:CYS841 4.7 26.5 1.0 CB B:LYS843 4.7 42.3 1.0 O B:CYS867 4.7 23.6 1.0 CB B:PHE869 4.7 22.9 1.0 C B:CYS844 4.7 26.4 1.0 O B:CYS844 4.9 29.9 1.0 N B:LYS843 4.9 38.2 1.0 CA B:LYS843 5.0 32.2 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