Chlorine in PDB 5nkd: Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2I

All present enzymatic activity of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2I:
2.7.10.1;

The structure of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2I, PDB code: 5nkd was solved by D.Kudlinzki, V.L.Linhard, K.Witt, S.L.Gande, K.Saxena, S.Heinzlmeir, G.Medard, B.Kuester, H.Schwalbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.13 / 1.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.753, 107.477, 40.576, 90.00, 109.02, 90.00
R / Rfree (%)	18.4 / 22.4

The binding sites of Chlorine atom in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2I (pdb code 5nkd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2I, PDB code: 5nkd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1001 b:19.8 occ:0.52 CL1 A:91K1001 0.0 19.8 0.5 CBE A:91K1001 0.3 18.6 0.5 CBD A:91K1001 1.6 17.3 0.5 CAB A:91K1001 1.7 16.9 0.5 CBF A:91K1001 2.6 18.2 0.5 CAC A:91K1001 2.6 14.9 0.5 CAC A:91K1001 2.7 14.9 0.5 CBH A:91K1001 2.7 18.9 0.5 NAD A:91K1001 2.9 13.7 0.5 NAD A:91K1001 3.0 13.7 0.5 CAE A:91K1001 3.3 12.2 0.5 CAE A:91K1001 3.3 12.2 0.5 OBC A:91K1001 3.4 13.8 0.5 OBC A:91K1001 3.4 13.7 0.5 CB A:SER756 3.6 17.4 1.0 O A:HOH1250 3.6 36.7 1.0 O A:HOH1193 3.8 27.3 1.0 CBG A:91K1001 3.9 15.9 0.5 CAB A:91K1001 3.9 14.2 0.5 CBD A:91K1001 4.0 14.3 0.5 CBG A:91K1001 4.0 15.5 0.5 CD1 A:LEU746 4.0 10.7 1.0 CG2 A:ILE676 4.2 16.8 1.0 CAF A:91K1001 4.2 11.4 0.5 CAF A:91K1001 4.2 11.3 0.5 CG1 A:ILE676 4.3 19.3 1.0 CBH A:91K1001 4.4 17.2 0.5 OG A:SER756 4.4 26.4 1.0 O A:HOH1228 4.4 37.1 1.0 N A:ASP757 4.5 16.2 1.0 CB A:ILE676 4.5 12.6 1.0 CBF A:91K1001 4.5 17.0 0.5 CA A:SER756 4.6 9.9 1.0 OE2 A:GLU663 4.7 25.9 1.0 O A:HOH1219 4.8 30.6 1.0 CAG A:91K1001 4.8 12.4 0.5 CAG A:91K1001 4.8 12.4 0.5 SD A:MET667 5.0 31.9 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2I


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2I within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1001 b:18.1 occ:0.46 CL1 A:91K1001 0.0 18.1 0.5 CBE A:91K1001 0.3 18.2 0.5 CBD A:91K1001 1.6 14.3 0.5 CAB A:91K1001 1.8 14.2 0.5 CBF A:91K1001 2.5 17.0 0.5 CAC A:91K1001 2.7 14.9 0.5 CBH A:91K1001 2.7 17.2 0.5 CAC A:91K1001 2.8 14.9 0.5 NAD A:91K1001 3.0 13.7 0.5 NAD A:91K1001 3.1 13.7 0.5 O A:ALA644 3.3 15.4 1.0 O A:ILE690 3.4 16.9 1.0 N A:LYS646 3.5 12.9 1.0 C A:ALA644 3.5 16.0 1.0 N A:ILE645 3.6 13.8 1.0 CB A:ALA644 3.7 16.1 1.0 CB A:LYS646 3.7 16.4 1.0 CAE A:91K1001 3.7 12.2 0.5 OG1 A:THR692 3.8 12.9 1.0 CAE A:91K1001 3.8 12.2 0.5 C A:ILE645 3.8 15.5 1.0 CBG A:91K1001 3.8 15.5 0.5 CA A:ILE645 3.9 13.5 1.0 CAB A:91K1001 3.9 16.9 0.5 CG2 A:THR692 4.0 11.8 1.0 CBG A:91K1001 4.0 15.9 0.5 OBC A:91K1001 4.0 13.8 0.5 OBC A:91K1001 4.1 13.7 0.5 CBD A:91K1001 4.1 17.3 0.5 CA A:LYS646 4.1 13.0 1.0 CA A:ALA644 4.3 13.7 1.0 N A:THR692 4.3 14.0 1.0 C A:ILE690 4.3 16.8 1.0 CBH A:91K1001 4.4 18.9 0.5 CB A:THR692 4.4 12.9 1.0 CG1 A:VAL627 4.4 20.1 1.0 CBF A:91K1001 4.6 18.2 0.5 O A:ILE645 4.6 16.5 1.0 CAF A:91K1001 4.6 11.4 0.5 CAF A:91K1001 4.7 11.3 0.5 CA A:ILE691 4.8 17.6 1.0 C A:ILE691 4.9 16.9 1.0 N A:ILE691 4.9 15.3 1.0 CE A:LYS646 4.9 32.9 1.0 CA A:THR692 5.0 14.5 1.0

S.Heinzlmeir, J.Lohse, T.Treiber, D.Kudlinzki, V.Linhard, S.L.Gande, S.Sreeramulu, K.Saxena, X.Liu, M.Wilhelm, H.Schwalbe, B.Kuster, G.Medard. Chemoproteomics-Aided Medicinal Chemistry For the Discovery of EPHA2 Inhibitors. Chemmedchem V. 12 999 2017.
ISSN: ESSN 1860-7187
PubMed: 28544567
DOI: 10.1002/CMDC.201700217