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Chlorine in PDB 1rwq: Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine

Enzymatic activity of Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine

All present enzymatic activity of Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine:
3.4.14.5;

Protein crystallography data

The structure of Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine, PDB code: 1rwq was solved by M.Hennig, R.Thoma, M.Stihle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.676, 69.141, 422.559, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 29

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine (pdb code 1rwq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine, PDB code: 1rwq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 1rwq

Go back to Chlorine Binding Sites List in 1rwq
Chlorine binding site 1 out of 4 in the Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl900

b:58.4
occ:1.00
 CL2 A:5AP900 0.0 58.4 1.0
C17 A:5AP900 1.7 40.7 1.0
C11 A:5AP900 2.6 42.0 1.0
C16 A:5AP900 2.7 38.3 1.0
C10 A:5AP900 2.8 42.5 1.0
N21 A:5AP900 3.0 37.7 1.0
C19 A:5AP900 3.1 41.6 1.0
N9 A:5AP900 3.3 43.4 1.0
NH2 A:ARG125 3.4 30.3 1.0
ND2 A:ASN710 3.4 33.0 1.0
C20 A:5AP900 3.5 38.3 1.0
OE2 A:GLU205 3.5 33.1 1.0
O A:HOH945 3.5 32.7 1.0
OH A:TYR662 3.6 35.5 1.0
OG A:SER630 3.8 37.0 1.0
NE2 A:HIS740 3.8 32.7 1.0
C14 A:5AP900 3.9 35.6 1.0
CD2 A:HIS740 3.9 29.6 1.0
C12 A:5AP900 3.9 41.9 1.0
C22 A:5AP900 3.9 44.6 1.0
O A:HOH905 3.9 35.4 1.0
C2 A:5AP900 4.0 44.2 1.0
CG A:ASN710 4.1 33.5 1.0
OD1 A:ASN710 4.1 33.3 1.0
N1 A:5AP900 4.3 44.4 1.0
C13 A:5AP900 4.4 37.9 1.0
CZ A:TYR662 4.6 32.9 1.0
CZ A:ARG125 4.7 34.9 1.0
CD A:GLU205 4.8 29.1 1.0
N23 A:5AP900 4.8 42.7 1.0
CE1 A:HIS740 4.9 31.0 1.0
CB A:SER630 5.0 33.3 1.0

Chlorine binding site 2 out of 4 in 1rwq

Go back to Chlorine Binding Sites List in 1rwq
Chlorine binding site 2 out of 4 in the Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl900

b:43.5
occ:1.00
 CL1 A:5AP900 0.0 43.5 1.0
C14 A:5AP900 1.7 35.6 1.0
C16 A:5AP900 2.6 38.3 1.0
C13 A:5AP900 2.7 37.9 1.0
CH2 A:TRP659 3.8 30.9 1.0
CG2 A:VAL656 3.8 29.4 1.0
C17 A:5AP900 3.9 40.7 1.0
CD2 A:TYR631 3.9 31.3 1.0
C12 A:5AP900 4.0 41.9 1.0
N A:TYR631 4.0 31.9 1.0
CE2 A:TYR662 4.1 33.0 1.0
CA A:TYR631 4.1 30.4 1.0
CZ3 A:TRP659 4.1 29.5 1.0
CB A:TYR631 4.2 30.6 1.0
CE1 A:TYR666 4.2 33.5 1.0
OG A:SER630 4.3 37.0 1.0
CD2 A:TYR662 4.3 31.4 1.0
CZ A:TYR666 4.4 33.1 1.0
C11 A:5AP900 4.4 42.0 1.0
OH A:TYR666 4.4 40.1 1.0
CZ A:TYR662 4.5 32.9 1.0
CG A:TYR631 4.5 30.3 1.0
C A:SER630 4.6 31.9 1.0
CB A:VAL656 4.7 31.8 1.0
CG2 A:VAL711 4.8 28.1 1.0
CD1 A:TYR666 4.8 33.3 1.0
CG A:TYR662 4.8 28.5 1.0
CZ2 A:TRP659 4.9 28.2 1.0
OH A:TYR662 4.9 35.5 1.0
CE2 A:TYR631 4.9 32.1 1.0

Chlorine binding site 3 out of 4 in 1rwq

Go back to Chlorine Binding Sites List in 1rwq
Chlorine binding site 3 out of 4 in the Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1900

b:63.9
occ:1.00
 CL2 B:5AP1900 0.0 63.9 1.0
C17 B:5AP1900 1.7 44.8 1.0
C16 B:5AP1900 2.6 43.0 1.0
C11 B:5AP1900 2.7 43.3 1.0
C10 B:5AP1900 3.1 41.6 1.0
ND2 B:ASN710 3.1 33.6 1.0
N21 B:5AP1900 3.3 38.9 1.0
OH B:TYR662 3.4 34.5 1.0
OE2 B:GLU205 3.5 29.9 1.0
NH2 B:ARG125 3.6 27.8 1.0
C19 B:5AP1900 3.6 39.4 1.0
N9 B:5AP1900 3.6 40.0 1.0
CG B:ASN710 3.7 31.9 1.0
OD1 B:ASN710 3.8 29.7 1.0
CD2 B:HIS740 3.8 25.8 1.0
O B:HOH1951 3.8 42.0 1.0
C14 B:5AP1900 3.9 41.4 1.0
O B:HOH1906 3.9 35.9 1.0
NE2 B:HIS740 3.9 27.2 1.0
C20 B:5AP1900 3.9 39.1 1.0
C12 B:5AP1900 4.0 38.6 1.0
OG B:SER630 4.0 36.3 1.0
C13 B:5AP1900 4.4 42.3 1.0
C2 B:5AP1900 4.4 42.2 1.0
C22 B:5AP1900 4.5 39.4 1.0
CZ B:TYR662 4.5 34.6 1.0
CD B:GLU205 4.6 28.8 1.0
CG2 B:VAL711 4.8 25.5 1.0
N1 B:5AP1900 4.8 39.5 1.0
CG B:HIS740 4.8 28.7 1.0
CZ B:ARG125 4.9 33.2 1.0
CE1 B:HIS740 5.0 23.5 1.0
CB B:ASN710 5.0 29.7 1.0

Chlorine binding site 4 out of 4 in 1rwq

Go back to Chlorine Binding Sites List in 1rwq
Chlorine binding site 4 out of 4 in the Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human Dipeptidyl Peptidase IV in Complex with 5-Aminomethyl-6-(2,4- Dichloro-Phenyl)-2-(3,5-Dimethoxy-Phenyl)-Pyrimidin-4-Ylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1900

b:45.9
occ:1.00
 CL1 B:5AP1900 0.0 45.9 1.0
C14 B:5AP1900 1.8 41.4 1.0
C13 B:5AP1900 2.7 42.3 1.0
C16 B:5AP1900 2.7 43.0 1.0
CG2 B:VAL656 3.4 32.5 1.0
CD2 B:TYR631 3.7 30.4 1.0
CB B:TYR631 3.8 32.4 1.0
CA B:TYR631 3.9 31.4 1.0
CH2 B:TRP659 4.0 29.5 1.0
C17 B:5AP1900 4.0 44.8 1.0
N B:TYR631 4.0 32.3 1.0
C12 B:5AP1900 4.0 38.6 1.0
CE2 B:TYR662 4.1 34.0 1.0
CZ3 B:TRP659 4.2 21.4 1.0
CG B:TYR631 4.3 30.5 1.0
OG B:SER630 4.3 36.3 1.0
CZ B:TYR662 4.3 34.6 1.0
CD2 B:TYR662 4.3 34.2 1.0
CE1 B:TYR666 4.4 28.5 1.0
OH B:TYR666 4.5 34.2 1.0
C11 B:5AP1900 4.5 43.3 1.0
CZ B:TYR666 4.6 30.8 1.0
OH B:TYR662 4.6 34.5 1.0
CB B:VAL656 4.7 33.4 1.0
CE1 B:TYR662 4.7 31.3 1.0
CE2 B:TYR631 4.8 32.4 1.0
CG B:TYR662 4.8 31.4 1.0
C B:SER630 4.8 32.8 1.0
CG2 B:VAL711 4.9 25.5 1.0
CD1 B:TYR662 4.9 28.6 1.0

Reference:

J.U.Peters, S.Weber, S.Kritter, P.Weiss, A.Wallier, M.Boehringer, M.Hennig, B.Kuhn, B.M.Loeffler. Aminomethylpyrimidines As Novel Dpp-IV Inhibitors: A 10(5)-Fold Activity Increase By Optimization of Aromatic Substituents Bioorg.Med.Chem.Lett. V. 14 1491 2004.
ISSN: ISSN 0960-894X
PubMed: 15006388
DOI: 10.1016/J.BMCL.2004.01.019
Page generated: Sat Jul 20 02:00:29 2024

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