Chlorine in PDB 5mja: Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor

All present enzymatic activity of Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor:
2.7.10.1;

The structure of Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor, PDB code: 5mja was solved by A.Kung, M.Schimpl, Y.-C.Chen, R.C.Overman, C.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.89 / 2.14
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.806, 101.806, 157.140, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 23.6

The binding sites of Chlorine atom in the Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor (pdb code 5mja). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor, PDB code: 5mja:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl901 b:45.5 occ:1.00 CL1 A:7O3901 0.0 45.5 1.0 C15 A:7O3901 1.7 44.6 1.0 C14 A:7O3901 2.7 40.5 1.0 C10 A:7O3901 2.7 45.7 1.0 N3 A:7O3901 3.0 46.2 1.0 OG1 A:THR697 3.3 39.0 1.0 C9 A:7O3901 3.5 44.9 1.0 N2 A:7O3901 3.5 46.4 1.0 N A:LYS651 3.6 41.0 1.0 C A:ALA649 3.7 39.0 1.0 CB A:ALA649 3.7 33.3 1.0 O A:ALA649 3.7 39.0 1.0 N A:ILE650 3.8 39.2 1.0 CG1 A:VAL633 3.8 46.0 1.0 CG A:LYS651 3.9 50.1 1.0 C A:ILE650 3.9 44.6 1.0 C13 A:7O3901 4.0 40.7 1.0 C11 A:7O3901 4.0 44.0 1.0 CB A:LYS651 4.0 42.6 1.0 O A:ILE695 4.1 40.2 1.0 CA A:ILE650 4.1 39.1 1.0 CG2 A:THR697 4.2 36.9 1.0 CA A:LYS651 4.2 41.5 1.0 CA A:ALA649 4.3 34.2 1.0 CB A:THR697 4.3 42.1 1.0 C12 A:7O3901 4.5 44.4 1.0 C2 A:7O3901 4.5 47.6 1.0 C8 A:7O3901 4.6 46.0 1.0 O A:ILE650 4.7 44.9 1.0 N A:THR697 4.7 33.5 1.0 CD A:LYS651 4.7 49.8 1.0 CG2 A:VAL633 4.9 46.7 1.0 CB A:VAL633 5.0 47.6 1.0

Chlorine binding site 2 out of 4 in the Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl901 b:57.5 occ:0.10 CL A:7O3901 0.0 57.5 0.1 C7 A:7O3901 1.8 58.6 1.0 C6 A:7O3901 2.8 58.6 1.0 N A:7O3901 2.9 50.8 1.0 O A:HOH1070 3.5 49.6 1.0 CA A:GLY703 3.6 39.1 1.0 O A:7O3901 3.9 60.8 1.0 O A:ILE625 4.2 58.3 1.0 C5 A:7O3901 4.2 49.2 1.0 N A:GLY703 4.2 39.8 1.0 O A:ASN702 4.5 39.9 1.0 N A:ALA704 4.5 36.0 1.0 C A:GLY703 4.6 39.6 1.0 C A:ASN702 4.6 40.9 1.0 C A:7O3901 4.8 47.5 1.0

Chlorine binding site 3 out of 4 in the Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl901 b:49.0 occ:1.00 CL1 B:7O3901 0.0 49.0 1.0 C15 B:7O3901 1.7 46.9 1.0 C14 B:7O3901 2.7 44.9 1.0 C10 B:7O3901 2.7 47.8 1.0 N3 B:7O3901 3.0 49.5 1.0 OG1 B:THR697 3.4 44.9 1.0 C9 B:7O3901 3.4 51.7 1.0 N2 B:7O3901 3.5 51.9 1.0 CB B:ALA649 3.7 40.4 1.0 CG1 B:VAL633 3.7 57.7 1.0 N B:LYS651 3.8 50.1 1.0 CG B:LYS651 3.8 54.9 1.0 C B:ALA649 3.9 45.7 1.0 C13 B:7O3901 4.0 45.1 1.0 O B:ALA649 4.0 42.9 1.0 C11 B:7O3901 4.0 47.5 1.0 N B:ILE650 4.0 47.0 1.0 CB B:LYS651 4.0 50.7 1.0 C B:ILE650 4.1 53.7 1.0 CA B:LYS651 4.3 50.3 1.0 O B:ILE695 4.4 48.2 1.0 CA B:ILE650 4.4 47.8 1.0 CG2 B:THR697 4.4 45.4 1.0 CA B:ALA649 4.4 41.1 1.0 C12 B:7O3901 4.5 46.5 1.0 CB B:THR697 4.5 45.8 1.0 CD B:LYS651 4.5 52.2 1.0 C2 B:7O3901 4.6 51.8 1.0 C8 B:7O3901 4.6 51.4 1.0 CG2 B:VAL633 4.7 59.8 1.0 CE B:LYS651 4.8 54.5 1.0 O B:ILE650 4.8 55.5 1.0 CB B:VAL633 4.8 60.4 1.0

Chlorine binding site 4 out of 4 in the Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Kinase Domain of Human EPHB1 Bound to A Quinazoline-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl901 b:54.3 occ:0.10 CL B:7O3901 0.0 54.3 0.1 C7 B:7O3901 1.8 56.4 1.0 C6 B:7O3901 2.8 59.1 1.0 O B:HOH1091 2.9 54.4 1.0 N B:7O3901 3.1 57.9 1.0 CA B:GLY703 3.5 40.1 1.0 O B:7O3901 3.9 58.9 1.0 O B:HOH1061 3.9 56.4 1.0 N B:GLY703 3.9 40.5 1.0 O B:ASN702 4.2 44.2 1.0 C B:ASN702 4.2 45.3 1.0 C5 B:7O3901 4.4 54.2 1.0 C B:GLY703 4.6 43.0 1.0 N B:ALA704 4.7 41.4 1.0 O B:GLU701 4.7 53.0 1.0

A.Kung, M.Schimpl, A.Ekanayake, Y.C.Chen, R.Overman, C.Zhang. A Chemical-Genetic Approach to Generate Selective Covalent Inhibitors of Protein Kinases. Acs Chem. Biol. V. 12 1499 2017.
ISSN: ESSN 1554-8937
PubMed: 28459525
DOI: 10.1021/ACSCHEMBIO.6B01083