Chlorine in PDB 3nox: Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone

The structure of Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone, PDB code: 3nox was solved by H.E.Klei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.62 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.451, 67.072, 420.443, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 26.4

The binding sites of Chlorine atom in the Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone (pdb code 3nox). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone, PDB code: 3nox:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone


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 Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1 b:58.8 occ:1.00 CL22 A:6A51 0.0 58.8 1.0 C21 A:6A51 1.7 40.2 1.0 C20 A:6A51 2.6 34.2 1.0 C14 A:6A51 2.7 40.5 1.0 C1 A:6A51 3.0 39.7 1.0 OH A:TYR662 3.3 36.0 1.0 ND2 A:ASN710 3.4 32.4 1.0 NH2 A:ARG125 3.4 33.0 1.0 OD1 A:ASN710 3.4 32.9 1.0 N5 A:6A51 3.5 38.5 1.0 N16 A:6A51 3.5 31.2 1.0 NE2 A:HIS740 3.6 30.9 1.0 CG A:ASN710 3.6 31.4 1.0 C2 A:6A51 3.6 38.2 1.0 CD2 A:HIS740 3.7 33.6 1.0 OG A:SER630 3.7 35.4 1.0 OE2 A:GLU205 3.8 25.7 1.0 C9 A:6A51 3.9 43.5 1.0 C19 A:6A51 3.9 38.3 1.0 C17 A:6A51 4.0 33.8 1.0 C15 A:6A51 4.1 37.2 1.0 C18 A:6A51 4.4 35.0 1.0 CZ A:TYR662 4.5 38.8 1.0 C6 A:6A51 4.5 39.4 1.0 O A:HOH904 4.5 41.5 1.0 CE1 A:HIS740 4.5 31.3 1.0 C3 A:6A51 4.6 35.1 1.0 CG A:HIS740 4.7 30.8 1.0 CZ A:ARG125 4.7 37.5 1.0 CB A:ASN710 4.8 29.6 1.0 C8 A:6A51 4.9 42.1 1.0 CD A:GLU205 4.9 38.8 1.0 N4 A:6A51 5.0 38.4 1.0 CE1 A:TYR662 5.0 31.4 1.0 CB A:SER630 5.0 31.7 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone


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 Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1 b:46.1 occ:1.00 CL23 A:6A51 0.0 46.1 1.0 C19 A:6A51 1.7 38.3 1.0 C20 A:6A51 2.6 34.2 1.0 C18 A:6A51 2.7 35.0 1.0 CG2 A:VAL656 3.3 27.2 1.0 C21 A:6A51 3.9 40.2 1.0 N A:TYR631 3.9 32.2 1.0 C17 A:6A51 4.0 33.8 1.0 CA A:TYR631 4.0 30.6 1.0 CB A:TYR631 4.1 29.9 1.0 CD2 A:TYR631 4.2 31.6 1.0 CH2 A:TRP659 4.2 29.4 1.0 CZ A:TYR662 4.2 38.8 1.0 CE2 A:TYR662 4.2 34.7 1.0 CZ3 A:TRP659 4.3 28.4 1.0 OG A:SER630 4.3 35.4 1.0 CB A:VAL656 4.4 31.7 1.0 C14 A:6A51 4.4 40.5 1.0 CD2 A:TYR662 4.5 32.9 1.0 CE1 A:TYR662 4.5 31.4 1.0 CG2 A:VAL711 4.5 26.5 1.0 C A:SER630 4.5 31.6 1.0 CG A:TYR631 4.6 29.9 1.0 OH A:TYR662 4.6 36.0 1.0 CD1 A:TYR662 4.7 27.4 1.0 CG A:TYR662 4.7 35.8 1.0 CE1 A:TYR666 4.8 28.0 1.0 O A:SER630 5.0 33.5 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2 b:61.3 occ:1.00 CL22 B:6A52 0.0 61.3 1.0 C21 B:6A52 1.7 44.2 1.0 C20 B:6A52 2.6 36.3 1.0 C14 B:6A52 2.7 40.2 1.0 C1 B:6A52 3.0 39.0 1.0 N5 B:6A52 3.3 40.2 1.0 ND2 B:ASN710 3.4 35.6 1.0 NH2 B:ARG125 3.4 37.2 1.0 NE2 B:HIS740 3.5 35.7 1.0 N16 B:6A52 3.5 32.6 1.0 CD2 B:HIS740 3.5 35.1 1.0 C2 B:6A52 3.6 35.9 1.0 C9 B:6A52 3.6 39.9 1.0 OG B:SER630 3.7 36.7 1.0 OH B:TYR662 3.8 38.5 1.0 C19 B:6A52 3.9 39.3 1.0 OE2 B:GLU205 3.9 29.6 1.0 O B:HOH820 4.0 32.1 1.0 CG B:ASN710 4.0 35.2 1.0 C17 B:6A52 4.0 37.5 1.0 OD1 B:ASN710 4.0 31.3 1.0 C15 B:6A52 4.2 32.2 1.0 C6 B:6A52 4.2 40.2 1.0 C3 B:6A52 4.4 38.1 1.0 C18 B:6A52 4.4 37.4 1.0 CE1 B:HIS740 4.5 35.0 1.0 C8 B:6A52 4.6 46.2 1.0 CG B:HIS740 4.6 35.3 1.0 CZ B:ARG125 4.7 35.5 1.0 N4 B:6A52 4.8 39.5 1.0 CB B:SER630 4.8 33.6 1.0 C24 B:6A52 4.9 44.6 1.0 CZ B:TYR662 4.9 37.0 1.0 N7 B:6A52 5.0 44.8 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Dpp-IV in Complex with Sa-(+)-(6- (Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2-A]Pyrimidin- 2-Yl)(Morpholino)Methanone within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2 b:48.2 occ:1.00 CL23 B:6A52 0.0 48.2 1.0 C19 B:6A52 1.7 39.3 1.0 C20 B:6A52 2.6 36.3 1.0 C18 B:6A52 2.7 37.4 1.0 CG2 B:VAL656 3.4 25.8 1.0 OG B:SER630 3.8 36.7 1.0 C21 B:6A52 3.8 44.2 1.0 C17 B:6A52 3.9 37.5 1.0 N B:TYR631 4.0 31.0 1.0 CZ B:TYR662 4.0 37.0 1.0 CE2 B:TYR662 4.2 33.1 1.0 CA B:TYR631 4.2 32.1 1.0 CE1 B:TYR662 4.2 33.6 1.0 CG2 B:VAL711 4.3 31.9 1.0 CB B:TYR631 4.4 27.8 1.0 C B:SER630 4.4 31.2 1.0 C14 B:6A52 4.4 40.2 1.0 OH B:TYR662 4.4 38.5 1.0 CH2 B:TRP659 4.4 31.4 1.0 CZ3 B:TRP659 4.4 27.0 1.0 CD2 B:TYR662 4.5 31.7 1.0 CD2 B:TYR631 4.5 23.4 1.0 CB B:VAL656 4.5 30.1 1.0 CD1 B:TYR662 4.5 23.8 1.0 CG B:TYR662 4.6 26.4 1.0 CE1 B:TYR666 4.8 30.2 1.0 O B:SER630 4.8 35.7 1.0 CG B:TYR631 4.9 24.6 1.0 CB B:SER630 4.9 33.6 1.0 CA B:SER630 4.9 29.9 1.0

W.Meng, R.P.Brigance, H.J.Chao, A.Fura, T.Harrity, J.Marcinkeviciene, S.P.O'connor, J.K.Tamura, D.Xie, Y.Zhang, H.E.Klei, K.Kish, C.A.Weigelt, H.Turdi, A.Wang, R.Zahler, M.S.Kirby, L.G.Hamann. Discovery of 6-(Aminomethyl)-5-(2,4-Dichlorophenyl)-7-Methylimidazo[1,2- A]Pyrimidine-2-Carboxamides As Potent, Selective Dipeptidyl Peptidase-4 (DPP4) Inhibitors. J.Med.Chem. V. 53 5620 2010.
ISSN: ISSN 0022-2623
PubMed: 20684603
DOI: 10.1021/JM100634A