Zinc in PDB 5fz0: Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 2,5-Dichloro-N-(Pyridin-3-Yl)Thiophene-3-Carboxamide (N08137B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening)

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 2,5-Dichloro-N-(Pyridin-3-Yl)Thiophene-3-Carboxamide (N08137B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening), PDB code: 5fz0 was solved by R.Nowak, T.Krojer, N.Pearce, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, F.Von Delft, P.E.Brennan, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.74 / 2.42
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.880, 143.880, 153.470, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 23.3

The structure of Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 2,5-Dichloro-N-(Pyridin-3-Yl)Thiophene-3-Carboxamide (N08137B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 2,5-Dichloro-N-(Pyridin-3-Yl)Thiophene-3-Carboxamide (N08137B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) (pdb code 5fz0). 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 the Catalytic Domain of Human JARID1B in Complex with 2,5-Dichloro-N-(Pyridin-3-Yl)Thiophene-3-Carboxamide (N08137B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening), PDB code: 5fz0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 2,5-Dichloro-N-(Pyridin-3-Yl)Thiophene-3-Carboxamide (N08137B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening)


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 the Catalytic Domain of Human JARID1B in Complex with 2,5-Dichloro-N-(Pyridin-3-Yl)Thiophene-3-Carboxamide (N08137B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1754 b:50.0 occ:1.00 ND1 A:HIS718 2.1 58.1 1.0 SG A:CYS692 2.2 48.3 1.0 SG A:CYS695 2.4 51.6 1.0 SG A:CYS715 2.4 51.0 1.0 CE1 A:HIS718 2.8 59.1 1.0 CB A:CYS692 3.1 47.3 1.0 CG A:HIS718 3.3 59.7 1.0 CB A:CYS695 3.3 48.4 1.0 CB A:CYS715 3.5 43.2 1.0 N A:CYS695 3.7 58.3 1.0 CB A:HIS718 3.8 47.7 1.0 N A:CYS715 3.8 47.0 1.0 NE2 A:HIS718 4.0 58.6 1.0 CA A:CYS695 4.1 50.1 1.0 CA A:CYS715 4.2 49.7 1.0 CD2 A:HIS718 4.3 54.6 1.0 CG2 A:THR697 4.4 42.9 1.0 N A:HIS718 4.5 50.2 1.0 CA A:CYS692 4.6 48.4 1.0 CB A:LYS694 4.6 53.4 1.0 CD A:ARG619 4.6 62.9 1.0 C A:CYS715 4.7 48.5 1.0 O A:CYS715 4.7 49.5 1.0 C A:CYS695 4.8 54.6 1.0 CA A:HIS718 4.8 51.5 1.0 C A:LYS694 4.9 59.4 1.0 CB A:HIS717 4.9 51.6 1.0 N A:LYS696 4.9 50.5 1.0 C A:VAL714 5.0 49.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with 2,5-Dichloro-N-(Pyridin-3-Yl)Thiophene-3-Carboxamide (N08137B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening)


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 the Catalytic Domain of Human JARID1B in Complex with 2,5-Dichloro-N-(Pyridin-3-Yl)Thiophene-3-Carboxamide (N08137B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1755 b:96.3 occ:1.00 CB A:CYS708 2.3 81.5 1.0 SG A:CYS723 2.5 75.6 1.0 SG A:CYS708 2.6 0.7 1.0 SG A:CYS706 2.6 71.6 1.0 SG A:CYS725 2.8 75.2 1.0 CB A:CYS725 3.3 61.4 1.0 CB A:CYS706 3.6 64.0 1.0 CB A:CYS723 3.6 62.7 1.0 CA A:CYS708 3.8 74.4 1.0 N A:CYS725 4.2 67.3 1.0 N A:CYS708 4.2 63.5 1.0 CE1 A:TYR730 4.3 65.2 1.0 CA A:CYS725 4.4 68.3 1.0 C A:CYS708 4.5 83.4 1.0 N A:LYS709 4.6 78.6 1.0 N A:SER724 4.8 69.4 1.0 CA A:CYS706 4.9 65.5 1.0 CA A:CYS723 4.9 67.7 1.0

R.Nowak, T.Krojer, C.Johansson, C.Gileadi, K.Kupinska, C.Strain-Damerell, A.Szykowska, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, F.Von Delft, P.E.Brennan, U.Oppermann. Crystal Structure of the Catalytic Domain of Human JARID1B in Complex with N11213A To Be Published.