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Chlorine in PDB 3g0c: Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1

Enzymatic activity of Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1

All present enzymatic activity of Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1:
3.4.14.5;

Protein crystallography data

The structure of Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1, PDB code: 3g0c was solved by Z.Zhang, M.B.Wallace, J.Feng, J.A.Stafford, S.W.Kaldor, L.Shi, R.J.Skene, K.Aertgeerts, B.Lee, A.Jennings, R.Xu, D.Kassel, D.R.Webb, S.L.Gwaltney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 122.844, 122.774, 145.106, 90.00, 114.68, 90.00
R / Rfree (%) 19.5 / 24.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1 (pdb code 3g0c). 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 Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1, PDB code: 3g0c:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3g0c

Go back to Chlorine Binding Sites List in 3g0c
Chlorine binding site 1 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1


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 Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl800

b:59.2
occ:1.00
 CL20 A:RUF800 0.0 59.2 1.0
C19 A:RUF800 1.7 58.0 1.0
C14 A:RUF800 2.7 57.2 1.0
C18 A:RUF800 2.7 58.2 1.0
C13 A:RUF800 3.0 56.2 1.0
CB A:TYR631 3.8 43.2 1.0
CD1 A:TYR631 3.9 43.3 1.0
C15 A:RUF800 4.0 58.1 1.0
C17 A:RUF800 4.0 58.2 1.0
N A:TYR631 4.0 44.0 1.0
CE2 A:TYR666 4.0 42.5 1.0
CE2 A:TYR662 4.1 38.7 1.0
CG2 A:VAL656 4.2 41.8 1.0
CA A:TYR631 4.2 43.0 1.0
CZ A:TYR666 4.2 42.7 1.0
CZ A:TYR662 4.2 40.0 1.0
OH A:TYR666 4.3 43.7 1.0
OH A:TYR662 4.3 40.5 1.0
CG A:TYR631 4.4 43.2 1.0
CH2 A:TRP659 4.4 41.7 1.0
N12 A:RUF800 4.4 56.0 1.0
C16 A:RUF800 4.5 58.4 1.0
CZ3 A:TRP659 4.5 41.9 1.0
CD2 A:TYR666 4.6 42.1 1.0
CD2 A:TYR662 4.6 39.5 1.0
O23 A:RUF800 4.7 55.1 1.0
C A:SER630 4.7 44.5 1.0
CB A:SER630 4.8 44.6 1.0
C11 A:RUF800 4.8 52.9 1.0
CE1 A:TYR662 4.9 39.4 1.0
CE1 A:TYR666 4.9 41.8 1.0
CE1 A:TYR631 5.0 43.0 1.0

Chlorine binding site 2 out of 4 in 3g0c

Go back to Chlorine Binding Sites List in 3g0c
Chlorine binding site 2 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1


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 Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl800

b:59.7
occ:1.00
 CL20 B:RUF800 0.0 59.7 1.0
C19 B:RUF800 1.7 57.5 1.0
C18 B:RUF800 2.7 58.4 1.0
C14 B:RUF800 2.7 57.0 1.0
C13 B:RUF800 3.0 56.1 1.0
CG2 B:VAL656 3.8 41.2 1.0
CE2 B:TYR662 3.8 42.3 1.0
CZ B:TYR662 4.0 42.6 1.0
C17 B:RUF800 4.0 59.0 1.0
C15 B:RUF800 4.0 58.4 1.0
CE2 B:TYR666 4.1 42.0 1.0
N B:TYR631 4.1 41.4 1.0
CH2 B:TRP659 4.2 39.7 1.0
OH B:TYR662 4.2 42.6 1.0
CZ B:TYR666 4.3 42.5 1.0
CB B:TYR631 4.3 40.7 1.0
CD2 B:TYR662 4.3 42.3 1.0
CD1 B:TYR631 4.3 40.3 1.0
CZ3 B:TRP659 4.3 39.8 1.0
CA B:TYR631 4.4 40.8 1.0
OH B:TYR666 4.4 42.3 1.0
N12 B:RUF800 4.5 55.9 1.0
C16 B:RUF800 4.5 59.3 1.0
CE1 B:TYR662 4.5 41.8 1.0
CD2 B:TYR666 4.6 42.1 1.0
C B:SER630 4.7 41.9 1.0
CB B:SER630 4.7 42.2 1.0
C11 B:RUF800 4.8 54.2 1.0
CG B:TYR631 4.8 40.7 1.0
CG B:TYR662 4.8 41.4 1.0
O23 B:RUF800 4.9 55.8 1.0
CD1 B:TYR662 4.9 41.2 1.0
CE1 B:TYR666 4.9 41.9 1.0

Chlorine binding site 3 out of 4 in 3g0c

Go back to Chlorine Binding Sites List in 3g0c
Chlorine binding site 3 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1


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 Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl800

b:56.1
occ:1.00
 CL20 C:RUF800 0.0 56.1 1.0
C19 C:RUF800 1.7 54.6 1.0
C18 C:RUF800 2.7 54.9 1.0
C14 C:RUF800 2.7 55.2 1.0
C13 C:RUF800 3.1 54.4 1.0
CE2 C:TYR666 3.7 38.5 1.0
C17 C:RUF800 4.0 55.6 1.0
CE2 C:TYR662 4.0 41.3 1.0
CD1 C:TYR631 4.0 38.5 1.0
C15 C:RUF800 4.0 55.9 1.0
N C:TYR631 4.0 40.6 1.0
CG2 C:VAL656 4.0 42.3 1.0
CZ C:TYR666 4.1 39.7 1.0
CB C:TYR631 4.1 40.1 1.0
CH2 C:TRP659 4.2 40.3 1.0
OH C:TYR666 4.2 39.3 1.0
CA C:TYR631 4.2 40.1 1.0
CZ C:TYR662 4.3 41.2 1.0
CD2 C:TYR666 4.3 38.7 1.0
CZ3 C:TRP659 4.3 40.2 1.0
CD2 C:TYR662 4.4 41.6 1.0
C16 C:RUF800 4.5 56.0 1.0
N12 C:RUF800 4.5 53.8 1.0
OH C:TYR662 4.5 42.4 1.0
CG C:TYR631 4.5 39.2 1.0
C C:SER630 4.7 41.2 1.0
O23 C:RUF800 4.8 55.9 1.0
CE1 C:TYR662 4.9 41.7 1.0
C11 C:RUF800 4.9 54.3 1.0
CB C:SER630 4.9 41.5 1.0
CE1 C:TYR666 5.0 39.5 1.0
CG C:TYR662 5.0 41.9 1.0

Chlorine binding site 4 out of 4 in 3g0c

Go back to Chlorine Binding Sites List in 3g0c
Chlorine binding site 4 out of 4 in the Crystal Structure of Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1


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 Dipeptidyl Peptidase IV in Complex with A Pyrimidinedione Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl800

b:55.1
occ:1.00
 CL20 D:RUF800 0.0 55.1 1.0
C19 D:RUF800 1.7 54.7 1.0
C18 D:RUF800 2.7 54.1 1.0
C14 D:RUF800 2.7 54.3 1.0
C13 D:RUF800 3.1 53.8 1.0
CE2 D:TYR666 3.7 39.4 1.0
CD1 D:TYR631 3.7 38.9 1.0
CB D:TYR631 3.8 39.6 1.0
C17 D:RUF800 4.0 54.6 1.0
C15 D:RUF800 4.0 55.3 1.0
CE2 D:TYR662 4.0 40.7 1.0
N D:TYR631 4.1 41.1 1.0
CZ D:TYR666 4.1 39.6 1.0
CA D:TYR631 4.2 40.5 1.0
CG2 D:VAL656 4.2 42.4 1.0
CH2 D:TRP659 4.2 43.7 1.0
CD2 D:TYR666 4.2 39.3 1.0
CG D:TYR631 4.3 38.8 1.0
CZ D:TYR662 4.3 41.5 1.0
OH D:TYR666 4.3 40.0 1.0
CZ3 D:TRP659 4.3 43.4 1.0
OH D:TYR662 4.5 42.6 1.0
CD2 D:TYR662 4.5 40.9 1.0
N12 D:RUF800 4.5 54.1 1.0
C16 D:RUF800 4.5 54.8 1.0
O23 D:RUF800 4.8 53.4 1.0
CE1 D:TYR631 4.8 39.0 1.0
CE1 D:TYR662 4.9 40.9 1.0
C D:SER630 4.9 41.3 1.0
CE1 D:TYR666 5.0 38.5 1.0
C11 D:RUF800 5.0 51.8 1.0
CB D:SER630 5.0 41.4 1.0

Reference:

Z.Zhang, M.B.Wallace, J.Feng, J.A.Stafford, R.J.Skene, L.Shi, B.Lee, K.Aertgeerts, A.Jennings, R.Xu, D.B.Kassel, S.W.Kaldor, M.Navre, D.R.Webb, S.L.Gwaltney. Design and Synthesis of Pyrimidinone and Pyrimidinedione Inhibitors of Dipeptidyl Peptidase IV. J.Med.Chem. V. 54 510 2011.
ISSN: ISSN 0022-2623
PubMed: 21186796
DOI: 10.1021/JM101016W
Page generated: Sat Jul 20 19:52:49 2024

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