Zinc in PDB 4yab: Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1)

The structure of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1), PDB code: 4yab 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)	60.56 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.640, 36.950, 128.921, 90.00, 110.03, 90.00
R / Rfree (%)	16.1 / 21.9

The binding sites of Zinc atom in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1) (pdb code 4yab). 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 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1), PDB code: 4yab:
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 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1)


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 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:24.8 occ:1.00 SG A:CYS852 2.2 25.4 1.0 ND1 A:HIS849 2.3 30.5 1.0 SG A:CYS829 2.4 24.0 1.0 SG A:CYS832 2.4 24.1 1.0 CB A:CYS829 3.1 25.2 1.0 CB A:CYS852 3.2 22.5 1.0 CE1 A:HIS849 3.2 32.8 1.0 CG A:HIS849 3.3 30.6 1.0 CB A:CYS832 3.3 25.7 1.0 CB A:HIS849 3.5 26.4 1.0 N A:CYS832 3.9 23.0 1.0 N A:HIS849 4.0 24.5 1.0 CA A:CYS832 4.2 22.1 1.0 NE2 A:HIS849 4.4 31.4 1.0 CA A:HIS849 4.4 24.7 1.0 CD2 A:HIS849 4.4 33.2 1.0 O A:HOH1400 4.5 69.3 1.0 CA A:CYS829 4.6 26.9 1.0 CB A:VAL831 4.6 21.4 1.0 CA A:CYS852 4.6 22.6 1.0 O A:HOH1334 4.7 40.1 1.0 C A:CYS832 4.9 22.0 1.0 C A:VAL831 4.9 24.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1)


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 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:27.7 occ:1.00 SG A:CYS870 2.3 28.3 1.0 SG A:CYS841 2.4 29.3 1.0 SG A:CYS844 2.4 28.8 1.0 SG A:CYS867 2.4 24.6 1.0 CB A:CYS841 3.2 31.0 1.0 CB A:CYS870 3.3 25.7 1.0 CB A:CYS844 3.3 28.2 1.0 CB A:CYS867 3.4 22.5 1.0 N A:CYS844 3.9 30.1 1.0 N A:CYS867 4.0 25.1 1.0 N A:CYS870 4.1 24.1 1.0 CA A:CYS844 4.1 30.2 1.0 CA A:CYS867 4.2 23.9 1.0 CA A:CYS870 4.3 27.4 1.0 O A:HOH1260 4.4 37.2 1.0 O A:HOH1281 4.4 58.9 1.0 C A:LYS843 4.5 36.0 1.0 C A:CYS867 4.7 23.0 1.0 CA A:CYS841 4.7 33.3 1.0 CB A:PHE869 4.7 22.4 1.0 O A:CYS867 4.7 23.2 1.0 C A:CYS844 4.7 28.1 1.0 CB A:LYS843 4.8 39.8 1.0 N A:LYS843 4.8 38.9 1.0 O A:CYS844 4.8 33.0 1.0 CA A:LYS843 4.9 36.7 1.0 C A:PHE869 5.0 25.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1)


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 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:30.0 occ:1.00 SG B:CYS829 2.2 28.5 1.0 ND1 B:HIS849 2.3 45.7 1.0 SG B:CYS832 2.4 31.9 1.0 SG B:CYS852 2.5 28.4 1.0 CB B:CYS829 2.9 24.7 1.0 CE1 B:HIS849 3.1 33.2 1.0 CB B:CYS852 3.1 23.3 1.0 CB B:CYS832 3.2 30.1 1.0 CG B:HIS849 3.4 35.6 1.0 N B:CYS832 3.4 29.4 1.0 CB B:HIS849 3.8 32.9 1.0 CA B:CYS832 3.9 29.9 1.0 O A:HOH1375 4.1 55.5 1.0 N B:HIS849 4.1 32.5 1.0 NE2 B:HIS849 4.3 34.4 1.0 CB B:VAL831 4.3 26.3 1.0 CA B:CYS829 4.4 27.2 1.0 CD2 B:HIS849 4.5 35.3 1.0 C B:VAL831 4.5 30.2 1.0 CA B:CYS852 4.6 23.8 1.0 C B:CYS832 4.6 32.0 1.0 CA B:HIS849 4.6 31.7 1.0 N B:GLN833 4.7 31.9 1.0 N B:VAL831 4.7 27.6 1.0 CA B:VAL831 4.8 28.9 1.0 C B:CYS829 4.8 26.5 1.0 CG1 B:VAL831 4.8 29.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1)


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 1-Methyl-5- (2-Methyl-1 3-Thiazol-4-Yl)-2 3-Dihydro-1H-Indol-2-One (1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1102 b:34.5 occ:1.00 SG B:CYS841 2.2 35.4 1.0 SG B:CYS844 2.3 38.2 1.0 SG B:CYS870 2.3 36.4 1.0 SG B:CYS867 2.4 29.3 1.0 CB B:CYS841 3.1 36.4 1.0 CB B:CYS844 3.2 41.4 1.0 CB B:CYS870 3.3 29.3 1.0 CB B:CYS867 3.5 27.7 1.0 N B:CYS844 3.8 45.6 1.0 O B:HOH1252 3.9 50.6 1.0 N B:CYS867 4.0 30.4 1.0 CA B:CYS844 4.1 41.6 1.0 N B:CYS870 4.1 30.7 1.0 O B:HOH1258 4.2 52.0 1.0 CA B:CYS867 4.2 30.9 1.0 CA B:CYS870 4.3 29.7 1.0 C B:LYS843 4.5 50.6 1.0 CA B:CYS841 4.6 42.3 1.0 CB B:LYS843 4.6 58.8 1.0 C B:CYS844 4.7 37.5 1.0 O B:CYS867 4.7 29.1 1.0 O B:CYS844 4.8 40.7 1.0 C B:CYS867 4.8 27.7 1.0 CB B:PHE869 4.8 26.1 1.0 N B:LYS843 4.9 51.5 1.0 CA B:LYS843 4.9 48.7 1.0 C B:PHE869 5.0 27.3 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