Chlorine in PDB 3ccc: Crystal Structure of Human DPP4 in Complex with A Benzimidazole Derivative

All present enzymatic activity of Crystal Structure of Human DPP4 in Complex with A Benzimidazole Derivative:
3.4.14.5;

The structure of Crystal Structure of Human DPP4 in Complex with A Benzimidazole Derivative, PDB code: 3ccc was solved by M.B.Wallace, R.J.Skene, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.13 / 2.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	121.899, 121.958, 144.275, 90.00, 114.94, 90.00
R / Rfree (%)	20 / 26.7

The binding sites of Chlorine atom in the Crystal Structure of Human DPP4 in Complex with A Benzimidazole Derivative (pdb code 3ccc). 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 DPP4 in Complex with A Benzimidazole Derivative, PDB code: 3ccc:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Human DPP4 in Complex with A Benzimidazole Derivative


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 DPP4 in Complex with A Benzimidazole Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl800 b:60.6 occ:1.00 CL17 A:7AC800 0.0 60.6 1.0 C16 A:7AC800 1.7 58.6 1.0 C15 A:7AC800 2.7 58.2 1.0 C11 A:7AC800 2.7 58.7 1.0 C10 A:7AC800 2.9 58.2 1.0 N20 A:7AC800 3.0 59.3 1.0 OH A:TYR662 3.2 37.6 1.0 C18 A:7AC800 3.3 58.5 1.0 C19 A:7AC800 3.5 58.5 1.0 OD1 A:ASN710 3.6 34.2 1.0 C7 A:7AC800 3.6 58.5 1.0 ND2 A:ASN710 3.6 36.6 1.0 NE2 A:HIS740 3.7 39.9 1.0 CG A:ASN710 3.8 35.5 1.0 C14 A:7AC800 4.0 59.4 1.0 CD2 A:HIS740 4.0 38.1 1.0 C12 A:7AC800 4.0 59.7 1.0 C8 A:7AC800 4.1 59.0 1.0 CB A:SER630 4.1 41.5 1.0 NH2 A:ARG125 4.1 49.2 1.0 OG A:SER630 4.1 42.8 1.0 OE1 A:GLU205 4.2 54.5 1.0 C21 A:7AC800 4.2 59.0 1.0 CZ A:TYR662 4.2 38.6 1.0 C6 A:7AC800 4.4 58.5 1.0 C13 A:7AC800 4.5 60.3 1.0 CE1 A:HIS740 4.5 39.2 1.0 CG2 A:VAL711 4.6 33.2 1.0 C5 A:7AC800 4.7 58.8 1.0 N9 A:7AC800 4.7 58.5 1.0 CE1 A:TYR662 4.8 37.0 1.0 CB A:ASN710 4.9 36.8 1.0 CG A:HIS740 4.9 38.9 1.0 CE2 A:TYR662 5.0 39.0 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Human DPP4 in Complex with A Benzimidazole Derivative


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 DPP4 in Complex with A Benzimidazole Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl800 b:56.3 occ:1.00 CL17 B:7AC800 0.0 56.3 1.0 C16 B:7AC800 1.8 56.8 1.0 C15 B:7AC800 2.7 55.9 1.0 C11 B:7AC800 2.8 57.5 1.0 C10 B:7AC800 3.0 57.9 1.0 OH B:TYR662 3.3 36.0 1.0 N20 B:7AC800 3.3 56.9 1.0 NE2 B:HIS740 3.5 33.0 1.0 C7 B:7AC800 3.5 58.9 1.0 OD1 B:ASN710 3.5 34.8 1.0 C18 B:7AC800 3.5 58.4 1.0 C8 B:7AC800 3.8 59.1 1.0 CD2 B:HIS740 3.8 31.3 1.0 NH2 B:ARG125 3.9 54.9 1.0 C19 B:7AC800 3.9 58.3 1.0 CG B:ASN710 4.0 34.8 1.0 CB B:SER630 4.0 44.6 1.0 C14 B:7AC800 4.0 55.1 1.0 OG B:SER630 4.0 47.1 1.0 C12 B:7AC800 4.0 56.1 1.0 ND2 B:ASN710 4.1 35.7 1.0 OE1 B:GLU205 4.2 39.6 1.0 CE1 B:HIS740 4.3 32.6 1.0 N9 B:7AC800 4.3 59.4 1.0 C6 B:7AC800 4.4 58.8 1.0 CZ B:TYR662 4.4 36.4 1.0 C21 B:7AC800 4.4 58.7 1.0 C13 B:7AC800 4.5 55.6 1.0 CG2 B:VAL711 4.6 25.5 1.0 C5 B:7AC800 4.7 59.4 1.0 CG B:HIS740 4.8 32.3 1.0 CE1 B:TYR662 4.9 36.7 1.0 ND1 B:HIS740 5.0 31.4 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Human DPP4 in Complex with A Benzimidazole Derivative


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 DPP4 in Complex with A Benzimidazole Derivative within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl800 b:59.0 occ:1.00 CL17 C:7AC800 0.0 59.0 1.0 C16 C:7AC800 1.7 56.8 1.0 C15 C:7AC800 2.7 56.0 1.0 C11 C:7AC800 2.7 58.5 1.0 C10 C:7AC800 2.9 59.0 1.0 OH C:TYR662 3.2 40.0 1.0 C7 C:7AC800 3.5 59.6 1.0 NE2 C:HIS740 3.5 49.0 1.0 N20 C:7AC800 3.5 59.2 1.0 C18 C:7AC800 3.5 59.3 1.0 OD1 C:ASN710 3.7 47.9 1.0 C8 C:7AC800 3.8 59.4 1.0 CD2 C:HIS740 3.9 47.5 1.0 C19 C:7AC800 3.9 58.9 1.0 OE1 C:GLU205 3.9 47.9 1.0 C14 C:7AC800 3.9 57.2 1.0 CG C:ASN710 4.0 47.0 1.0 ND2 C:ASN710 4.0 48.2 1.0 C12 C:7AC800 4.0 58.1 1.0 CB C:SER630 4.0 46.9 1.0 OG C:SER630 4.2 51.7 1.0 CZ C:TYR662 4.2 40.2 1.0 NH2 C:ARG125 4.3 55.3 1.0 CG2 C:VAL711 4.3 44.1 1.0 O C:HOH841 4.3 49.0 1.0 C6 C:7AC800 4.4 59.2 1.0 N9 C:7AC800 4.4 59.0 1.0 C21 C:7AC800 4.4 59.5 1.0 CE1 C:HIS740 4.4 49.6 1.0 C13 C:7AC800 4.5 58.2 1.0 CE1 C:TYR662 4.8 39.7 1.0 C5 C:7AC800 4.8 59.4 1.0 CB C:ASN710 4.9 46.4 1.0 CG C:HIS740 4.9 47.1 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Human DPP4 in Complex with A Benzimidazole Derivative


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 DPP4 in Complex with A Benzimidazole Derivative within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl800 b:68.5 occ:1.00 CL17 D:7AC800 0.0 68.5 1.0 C16 D:7AC800 1.7 68.4 1.0 C11 D:7AC800 2.7 68.0 1.0 C15 D:7AC800 2.7 68.1 1.0 C10 D:7AC800 2.9 68.3 1.0 OD1 D:ASN710 3.3 54.1 1.0 C18 D:7AC800 3.3 68.2 1.0 OH D:TYR662 3.4 49.6 1.0 C7 D:7AC800 3.4 68.6 1.0 N20 D:7AC800 3.5 68.2 1.0 NE2 D:HIS740 3.6 48.5 1.0 C19 D:7AC800 3.7 68.3 1.0 C8 D:7AC800 3.8 68.5 1.0 CG D:ASN710 3.9 51.9 1.0 CD2 D:HIS740 4.0 48.8 1.0 CB D:SER630 4.0 52.0 1.0 NH2 D:ARG125 4.0 56.9 1.0 C12 D:7AC800 4.0 67.7 1.0 C14 D:7AC800 4.0 67.7 1.0 ND2 D:ASN710 4.1 51.7 1.0 OG D:SER630 4.2 53.8 1.0 C21 D:7AC800 4.2 68.4 1.0 C6 D:7AC800 4.3 68.2 1.0 OE1 D:GLU205 4.3 59.8 1.0 CZ D:TYR662 4.4 49.4 1.0 N9 D:7AC800 4.5 68.6 1.0 C13 D:7AC800 4.5 67.6 1.0 CE1 D:HIS740 4.5 48.7 1.0 C5 D:7AC800 4.6 68.4 1.0 CG2 D:VAL711 4.7 46.7 1.0 CE1 D:TYR662 4.9 48.6 1.0 CG D:HIS740 5.0 49.5 1.0

M.B.Wallace, J.Feng, Z.Zhang, R.J.Skene, L.Shi, C.L.Caster, D.B.Kassel, R.Xu, S.L.Gwaltney. Structure-Based Design and Synthesis of Benzimidazole Derivatives As Dipeptidyl Peptidase IV Inhibitors. Bioorg.Med.Chem.Lett. V. 18 2362 2008.
ISSN: ISSN 0960-894X
PubMed: 18346892
DOI: 10.1016/J.BMCL.2008.02.071