Zinc in PDB 5k4l: Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor

The structure of Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor, PDB code: 5k4l was solved by J.R.Kiefer, M.V.Vinogradova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.50 / 3.18
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	159.141, 159.141, 92.109, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 25.7

The structure of Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor (pdb code 5k4l). 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 KDM5A in Complex with A Naphthyridone Inhibitor, PDB code: 5k4l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor


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 KDM5A in Complex with A Naphthyridone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:0.2 occ:1.00 HB3 A:CYS699 1.2 89.1 1.0 HB2 A:CYS679 1.6 93.0 1.0 HB2 A:CYS676 1.8 70.2 1.0 CB A:CYS676 2.1 58.6 1.0 HB3 A:CYS676 2.1 70.2 1.0 CB A:CYS699 2.2 74.5 1.0 CB A:CYS679 2.2 77.7 1.0 SG A:CYS676 2.3 59.8 1.0 HB3 A:CYS679 2.3 93.0 1.0 H A:CYS699 2.5 87.8 1.0 HB2 A:CYS699 2.6 89.1 1.0 SG A:CYS679 2.7 56.2 1.0 SG A:CYS699 3.1 58.2 1.0 N A:CYS699 3.2 73.4 1.0 HG A:CYS679 3.2 67.2 1.0 CA A:CYS699 3.2 75.1 1.0 H A:THR681 3.3 95.2 1.0 HG A:CYS699 3.3 69.7 1.0 HB A:THR681 3.4 0.3 1.0 CA A:CYS676 3.6 59.3 1.0 CA A:CYS679 3.6 83.6 1.0 HA A:CYS699 3.9 89.9 1.0 HA A:CYS679 3.9 0.0 1.0 HA A:CYS676 3.9 70.9 1.0 N A:THR681 4.0 79.6 1.0 HA A:ARG680 4.0 0.5 1.0 N A:CYS679 4.1 88.7 1.0 H A:CYS676 4.1 69.7 1.0 HD1 A:HIS702 4.2 0.8 1.0 N A:CYS676 4.2 58.3 1.0 CB A:THR681 4.2 95.5 1.0 O A:THR681 4.3 71.7 1.0 C A:CYS699 4.3 75.9 1.0 HA A:VAL698 4.3 95.1 1.0 H A:CYS679 4.4 0.2 1.0 HB2 A:HIS702 4.4 0.8 1.0 O A:ALA678 4.4 0.5 1.0 SG A:CYS683 4.4 72.9 1.0 C A:VAL698 4.4 82.6 1.0 O A:CYS699 4.5 81.9 1.0 C A:CYS676 4.5 59.9 1.0 HG A:CYS683 4.5 87.3 1.0 C A:ALA678 4.5 0.5 1.0 HG22 A:VAL698 4.6 95.1 1.0 CA A:THR681 4.6 78.1 1.0 ND1 A:HIS702 4.6 0.7 1.0 OG1 A:THR681 4.7 98.7 1.0 C A:CYS679 4.8 98.5 1.0 CA A:ARG680 4.8 0.7 1.0 C A:ARG680 4.9 0.2 1.0 C A:THR681 4.9 74.2 1.0 CA A:VAL698 4.9 79.5 1.0 H A:SER677 5.0 0.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor


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 KDM5A in Complex with A Naphthyridone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:64.9 occ:1.00 H A:CYS692 2.0 0.2 1.0 HG A:CYS690 2.1 0.1 1.0 HB3 A:CYS692 2.2 0.0 1.0 SG A:CYS690 2.2 0.6 1.0 HB3 A:CYS690 2.3 0.5 1.0 SG A:CYS709 2.5 0.1 1.0 CB A:CYS690 2.7 0.6 1.0 N A:CYS692 2.8 0.8 1.0 H A:SER691 3.0 0.4 1.0 CB A:CYS692 3.0 0.7 1.0 HB3 A:CYS709 3.0 0.9 1.0 CB A:CYS709 3.2 0.4 1.0 N A:SER691 3.3 0.4 1.0 HB2 A:CYS690 3.4 0.5 1.0 CA A:CYS692 3.4 1.0 1.0 HB2 A:CYS709 3.4 0.9 1.0 SG A:CYS692 3.5 0.6 1.0 HB3 A:CYS707 3.7 0.1 1.0 C A:CYS690 3.7 0.2 1.0 CA A:CYS690 3.8 0.8 1.0 HB2 A:CYS692 3.8 0.0 1.0 HA A:CYS692 3.8 0.4 1.0 C A:SER691 3.9 99.9 1.0 CA A:SER691 4.1 0.6 1.0 HB2 A:CYS707 4.1 0.1 1.0 HD22 A:LEU706 4.2 0.8 1.0 CB A:CYS707 4.2 1.0 1.0 HA A:CYS690 4.4 0.1 1.0 HB2 A:SER691 4.4 0.5 1.0 SG A:CYS707 4.4 0.3 1.0 H A:ASN693 4.4 0.7 1.0 O A:CYS690 4.5 0.5 1.0 HG A:CYS692 4.6 0.5 1.0 H A:CYS709 4.6 0.9 1.0 CA A:CYS709 4.7 0.8 1.0 C A:CYS692 4.7 0.4 1.0 H A:CYS690 4.8 0.5 1.0 N A:CYS690 4.8 0.6 1.0 CB A:SER691 4.8 0.9 1.0 HA A:SER691 4.9 0.1 1.0 N A:ASN693 4.9 0.8 1.0 O A:SER691 5.0 84.6 1.0 HG A:CYS707 5.0 0.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor


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 KDM5A in Complex with A Naphthyridone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:24.4 occ:1.00 ND1 B:HIS702 2.0 0.3 1.0 SG B:CYS679 2.1 1.0 1.0 SG B:CYS699 2.3 0.1 1.0 SG B:CYS676 2.4 0.3 1.0 CE1 B:HIS702 2.7 0.4 1.0 HE1 B:HIS702 2.9 0.7 1.0 HB2 B:CYS679 2.9 0.5 1.0 CG B:HIS702 2.9 0.2 1.0 HB2 B:HIS702 3.0 0.8 1.0 CB B:CYS679 3.0 84.0 1.0 O B:ALA678 3.4 0.2 1.0 HA B:CYS679 3.4 0.7 1.0 H B:CYS699 3.4 0.8 1.0 CB B:HIS702 3.5 0.2 1.0 HB3 B:CYS676 3.6 0.2 1.0 NE2 B:HIS702 3.7 0.1 1.0 CB B:CYS676 3.7 0.8 1.0 CA B:CYS679 3.7 87.4 1.0 HB2 B:TYR701 3.7 0.5 1.0 CB B:CYS699 3.8 77.2 1.0 CD2 B:HIS702 3.8 0.2 1.0 H B:HIS702 3.8 0.2 1.0 HG22 B:VAL698 3.8 0.5 1.0 HB3 B:CYS679 3.9 0.5 1.0 HB2 B:CYS676 3.9 0.2 1.0 HB3 B:CYS699 3.9 92.4 1.0 HG1 B:THR681 3.9 0.2 1.0 N B:HIS702 4.0 0.0 1.0 C B:ALA678 4.1 0.4 1.0 N B:CYS699 4.1 95.0 1.0 N B:CYS679 4.2 88.5 1.0 HB3 B:HIS702 4.2 0.8 1.0 HD2 B:ARG603 4.2 0.9 1.0 HG3 B:ARG603 4.3 0.8 1.0 O B:CYS699 4.3 79.7 1.0 HE2 B:HIS702 4.4 0.3 1.0 CA B:CYS699 4.4 96.1 1.0 CA B:HIS702 4.4 0.4 1.0 H B:TYR701 4.4 0.4 1.0 CB B:TYR701 4.5 0.9 1.0 HB2 B:CYS699 4.5 92.4 1.0 HB3 B:TYR701 4.5 0.5 1.0 C B:TYR701 4.5 0.4 1.0 OG1 B:THR681 4.5 0.5 1.0 HD2 B:HIS702 4.6 0.5 1.0 C B:CYS699 4.6 99.5 1.0 CG2 B:VAL698 4.7 94.8 1.0 HG23 B:VAL698 4.8 0.5 1.0 H B:CYS679 4.9 0.9 1.0 HD3 B:ARG603 4.9 0.9 1.0 CD B:ARG603 4.9 0.8 1.0 CA B:TYR701 4.9 0.7 1.0 HA B:VAL698 4.9 0.0 1.0 N B:TYR701 4.9 0.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of KDM5A in Complex with A Naphthyridone Inhibitor


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 KDM5A in Complex with A Naphthyridone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn903 b:0.3 occ:1.00 HB3 B:CYS709 1.1 0.6 1.0 CB B:CYS709 2.1 0.7 1.0 SG B:CYS707 2.3 96.5 1.0 O B:CYS709 2.6 0.9 1.0 HB2 B:CYS709 2.6 0.6 1.0 H B:CYS709 2.6 0.5 1.0 CA B:CYS709 2.7 0.7 1.0 HG B:CYS707 2.8 0.6 1.0 HB3 B:CYS690 2.8 0.9 1.0 HG B:CYS692 2.8 0.5 1.0 N B:CYS709 2.9 0.5 1.0 C B:CYS709 3.0 0.4 1.0 SG B:CYS692 3.1 97.3 1.0 HB2 B:CYS690 3.2 0.9 1.0 CB B:CYS690 3.2 0.1 1.0 SG B:CYS690 3.3 0.4 1.0 O B:CYS707 3.3 92.2 1.0 SG B:CYS709 3.3 0.6 1.0 HG B:CYS709 3.5 0.7 1.0 HA B:CYS709 3.6 0.2 1.0 C B:CYS707 3.8 0.3 1.0 CB B:CYS707 3.9 0.0 1.0 C B:PRO708 4.0 0.4 1.0 HG B:CYS690 4.2 0.6 1.0 O B:PRO710 4.2 0.1 1.0 N B:PRO710 4.2 0.8 1.0 HB2 B:CYS707 4.4 0.4 1.0 CA B:CYS707 4.4 0.2 1.0 HD22 B:LEU706 4.4 0.1 1.0 H B:CYS692 4.4 0.3 1.0 N B:PRO708 4.4 0.9 1.0 HB3 B:CYS707 4.5 0.4 1.0 H B:CYS707 4.5 0.3 1.0 H B:SER691 4.6 0.0 1.0 CA B:CYS690 4.7 1.0 1.0 O B:PRO708 4.7 0.8 1.0 N B:CYS707 4.7 0.1 1.0 CB B:CYS692 4.7 88.9 1.0 HD13 B:LEU706 4.8 0.8 1.0 CA B:PRO708 4.8 0.9 1.0 HB2 B:CYS692 4.8 0.4 1.0 C B:PRO710 4.8 0.4 1.0 HB3 B:LEU706 4.9 0.2 1.0 HD2 B:PRO710 4.9 0.1 1.0

S.S.Labadie, P.S.Dragovich, R.T.Cummings, G.Deshmukh, A.Gustafson, N.Han, J.C.Harmange, J.R.Kiefer, Y.Li, J.Liang, B.M.Liederer, Y.Liu, W.Manieri, W.Mao, L.Murray, D.F.Ortwine, P.Trojer, E.Vanderporten, M.Vinogradova, L.Wen. Design and Evaluation of 1,7-Naphthyridones As Novel KDM5 Inhibitors. Bioorg.Med.Chem.Lett. V. 26 4492 2016.
ISSN: ESSN 1464-3405
PubMed: 27499454
DOI: 10.1016/J.BMCL.2016.07.070