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Bromine in PDB 5lls: Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione

Enzymatic activity of Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione

All present enzymatic activity of Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione:
3.4.14.5;

Protein crystallography data

The structure of Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione, PDB code: 5lls was solved by H.Nar, M.Blaesse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.28 / 2.41
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.900, 117.680, 133.120, 112.70, 94.60, 91.20
R / Rfree (%) 19 / 22.8

Bromine Binding Sites:

The binding sites of Bromine atom in the Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione (pdb code 5lls). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione, PDB code: 5lls:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 5lls

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Bromine binding site 1 out of 8 in the Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br809

b:46.9
occ:1.00
 BR A:6Z8809 0.0 46.9 1.0
C15 A:6Z8809 1.9 40.2 1.0
C22 A:6Z8809 2.8 37.5 1.0
C9 A:6Z8809 2.9 36.7 1.0
C4 A:6Z8809 3.2 32.1 1.0
CE1 A:TYR666 3.6 19.7 1.0
CZ A:TYR666 3.9 26.2 1.0
CD2 A:TYR631 3.9 17.2 1.0
OH A:TYR666 4.0 29.3 1.0
CH2 A:TRP659 4.0 23.2 1.0
CB A:TYR631 4.0 18.1 1.0
CE2 A:TYR662 4.1 19.6 1.0
C28 A:6Z8809 4.1 35.4 1.0
N A:TYR631 4.1 21.2 1.0
C16 A:6Z8809 4.1 36.0 1.0
CG2 A:VAL656 4.2 19.5 1.0
CD1 A:TYR666 4.2 21.0 1.0
CZ A:TYR662 4.2 20.9 1.0
CZ3 A:TRP659 4.2 22.3 1.0
CA A:TYR631 4.4 19.3 1.0
OH A:TYR662 4.4 18.1 1.0
CG A:TYR631 4.5 16.9 1.0
CE2 A:TYR666 4.6 21.1 1.0
CD2 A:TYR662 4.6 19.8 1.0
C24 A:6Z8809 4.6 34.6 1.0
N1 A:6Z8809 4.6 27.3 1.0
O12 A:6Z8809 4.8 24.7 1.0
CB A:SER630 4.8 30.3 1.0
CE1 A:TYR662 4.9 18.6 1.0
CG A:TYR666 4.9 19.4 1.0
C A:SER630 4.9 29.0 1.0
C13 A:6Z8809 4.9 34.4 1.0
CE2 A:TYR631 5.0 17.4 1.0

Bromine binding site 2 out of 8 in 5lls

Go back to Bromine Binding Sites List in 5lls
Bromine binding site 2 out of 8 in the Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br811

b:65.0
occ:0.66
 BR A:6Z8811 0.0 65.0 0.7
C15 A:6Z8811 1.9 51.4 0.7
C22 A:6Z8811 2.8 47.2 0.7
C9 A:6Z8811 2.9 43.4 0.7
C4 A:6Z8811 3.2 38.9 0.7
O A:ALA280 3.4 34.9 1.0
C A:ALA280 3.7 35.3 1.0
O A:PRO278 4.0 42.5 1.0
N A:ALA280 4.1 33.7 1.0
C A:ASN279 4.1 38.8 1.0
C28 A:6Z8811 4.1 44.7 0.7
C16 A:6Z8811 4.1 42.1 0.7
N27 A:6Z8811 4.2 36.1 0.7
N A:SER281 4.2 30.5 1.0
O A:ASN279 4.4 38.3 1.0
CA A:ALA280 4.4 32.6 1.0
CA A:SER281 4.5 27.8 1.0
CA A:ASN279 4.5 36.9 1.0
N1 A:6Z8811 4.6 35.4 0.7
C24 A:6Z8811 4.6 43.4 0.7
C A:PRO278 4.9 41.5 1.0
C26 A:6Z8811 5.0 36.3 0.7

Bromine binding site 3 out of 8 in 5lls

Go back to Bromine Binding Sites List in 5lls
Bromine binding site 3 out of 8 in the Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br809

b:43.4
occ:1.00
 BR B:6Z8809 0.0 43.4 1.0
C15 B:6Z8809 1.9 35.6 1.0
C22 B:6Z8809 2.8 34.3 1.0
C9 B:6Z8809 2.9 29.8 1.0
C4 B:6Z8809 3.2 25.9 1.0
CE1 B:TYR666 3.7 22.4 1.0
CD2 B:TYR631 3.9 21.6 1.0
CE2 B:TYR662 3.9 16.1 1.0
CZ B:TYR666 4.0 31.2 1.0
CG2 B:VAL656 4.0 19.4 1.0
CH2 B:TRP659 4.0 22.2 1.0
CZ B:TYR662 4.1 19.8 1.0
CB B:TYR631 4.1 21.7 1.0
C28 B:6Z8809 4.1 32.9 1.0
OH B:TYR666 4.1 29.7 1.0
C16 B:6Z8809 4.2 28.6 1.0
CZ3 B:TRP659 4.2 21.4 1.0
CD1 B:TYR666 4.2 20.0 1.0
N B:TYR631 4.2 22.3 1.0
OH B:TYR662 4.3 19.2 1.0
CA B:TYR631 4.3 21.4 1.0
CD2 B:TYR662 4.4 15.8 1.0
CG B:TYR631 4.5 21.1 1.0
N1 B:6Z8809 4.6 24.2 1.0
C24 B:6Z8809 4.7 31.0 1.0
CE1 B:TYR662 4.7 15.4 1.0
CE2 B:TYR666 4.7 21.9 1.0
O12 B:6Z8809 4.8 22.1 1.0
C B:SER630 4.9 27.2 1.0
CG B:TYR666 4.9 18.6 1.0
CE2 B:TYR631 5.0 22.5 1.0
CB B:SER630 5.0 28.2 1.0
C13 B:6Z8809 5.0 34.5 1.0
CG B:TYR662 5.0 15.7 1.0

Bromine binding site 4 out of 8 in 5lls

Go back to Bromine Binding Sites List in 5lls
Bromine binding site 4 out of 8 in the Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br811

b:68.6
occ:0.62
 BR B:6Z8811 0.0 68.6 0.6
C15 B:6Z8811 1.9 56.2 0.6
C22 B:6Z8811 2.8 51.8 0.6
C9 B:6Z8811 2.9 49.0 0.6
C4 B:6Z8811 3.1 44.0 0.6
O B:ALA280 3.4 32.6 1.0
C B:ALA280 3.7 32.2 1.0
N B:ALA280 4.0 31.2 1.0
C B:ASN279 4.0 36.6 1.0
O B:PRO278 4.1 39.7 1.0
N B:SER281 4.1 27.3 1.0
C28 B:6Z8811 4.1 49.7 0.6
C16 B:6Z8811 4.1 47.7 0.6
O B:ASN279 4.3 35.5 1.0
CA B:ALA280 4.3 29.4 1.0
O B:HOH1107 4.3 50.0 1.0
CA B:SER281 4.4 25.9 1.0
C13 B:6Z8811 4.5 42.8 0.6
CA B:ASN279 4.5 36.6 1.0
N1 B:6Z8811 4.5 39.3 0.6
C24 B:6Z8811 4.6 48.1 0.6
N8 B:6Z8811 5.0 42.1 0.6
C B:PRO278 5.0 41.5 1.0

Bromine binding site 5 out of 8 in 5lls

Go back to Bromine Binding Sites List in 5lls
Bromine binding site 5 out of 8 in the Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br808

b:44.2
occ:1.00
 BR C:6Z8808 0.0 44.2 1.0
C15 C:6Z8808 1.9 39.2 1.0
C22 C:6Z8808 2.8 37.2 1.0
C9 C:6Z8808 2.9 36.8 1.0
C4 C:6Z8808 3.2 31.7 1.0
O C:HOH927 3.2 37.0 1.0
CE1 C:TYR666 3.7 29.0 1.0
CZ C:TYR666 3.9 32.8 1.0
CE2 C:TYR662 4.0 23.5 1.0
CD2 C:TYR631 4.0 23.7 1.0
OH C:TYR666 4.1 32.4 1.0
CZ C:TYR662 4.1 29.1 1.0
CB C:TYR631 4.1 24.1 1.0
C28 C:6Z8808 4.1 36.9 1.0
CH2 C:TRP659 4.1 29.1 1.0
C16 C:6Z8808 4.1 38.6 1.0
OH C:TYR662 4.2 25.1 1.0
CG2 C:VAL656 4.2 24.5 1.0
CD1 C:TYR666 4.3 26.6 1.0
N C:TYR631 4.3 26.0 1.0
CZ3 C:TRP659 4.3 28.1 1.0
CA C:TYR631 4.4 24.9 1.0
CD2 C:TYR662 4.5 23.4 1.0
CG C:TYR631 4.5 23.8 1.0
N1 C:6Z8808 4.6 30.6 1.0
CE2 C:TYR666 4.6 22.7 1.0
C24 C:6Z8808 4.6 38.0 1.0
O12 C:6Z8808 4.7 28.6 1.0
CE1 C:TYR662 4.7 24.8 1.0
C C:SER630 4.9 31.9 1.0
CB C:SER630 4.9 28.5 1.0
CG C:TYR666 4.9 22.7 1.0
C13 C:6Z8808 5.0 31.4 1.0

Bromine binding site 6 out of 8 in 5lls

Go back to Bromine Binding Sites List in 5lls
Bromine binding site 6 out of 8 in the Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br810

b:85.8
occ:0.71
 BR C:6Z8810 0.0 85.8 0.7
C15 C:6Z8810 1.9 74.6 0.7
C22 C:6Z8810 2.8 72.1 0.7
C9 C:6Z8810 2.9 66.2 0.7
C4 C:6Z8810 3.2 58.0 0.7
O C:ALA280 3.4 25.4 1.0
O C:HOH1110 3.6 51.1 1.0
C C:ALA280 3.8 27.9 1.0
O C:PRO278 3.9 37.4 1.0
N C:ALA280 4.1 26.1 1.0
C28 C:6Z8810 4.1 70.1 0.7
C16 C:6Z8810 4.1 66.9 0.7
C C:ASN279 4.2 32.6 1.0
N C:SER281 4.3 26.3 1.0
C13 C:6Z8810 4.3 50.4 0.7
CA C:ALA280 4.4 25.1 1.0
CA C:SER281 4.5 25.7 1.0
O C:ASN279 4.5 32.9 1.0
N1 C:6Z8810 4.5 50.9 0.7
CA C:ASN279 4.5 31.0 1.0
C24 C:6Z8810 4.6 68.1 0.7
C C:PRO278 4.8 36.2 1.0
N8 C:6Z8810 4.9 50.7 0.7

Bromine binding site 7 out of 8 in 5lls

Go back to Bromine Binding Sites List in 5lls
Bromine binding site 7 out of 8 in the Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br811

b:49.7
occ:1.00
 BR D:6Z8811 0.0 49.7 1.0
C15 D:6Z8811 1.9 41.8 1.0
C22 D:6Z8811 2.8 38.4 1.0
C9 D:6Z8811 2.9 38.1 1.0
C4 D:6Z8811 3.2 36.0 1.0
CE1 D:TYR666 3.8 22.3 1.0
CZ D:TYR666 4.0 28.7 1.0
CE2 D:TYR662 4.0 23.3 1.0
CD2 D:TYR631 4.1 25.5 1.0
CG2 D:VAL656 4.1 23.7 1.0
CB D:TYR631 4.1 25.5 1.0
CZ D:TYR662 4.1 28.8 1.0
C28 D:6Z8811 4.1 38.0 1.0
OH D:TYR666 4.1 29.6 1.0
C16 D:6Z8811 4.1 35.6 1.0
CH2 D:TRP659 4.2 32.2 1.0
N D:TYR631 4.2 27.4 1.0
OH D:TYR662 4.3 27.4 1.0
CD1 D:TYR666 4.3 22.8 1.0
CA D:TYR631 4.4 26.4 1.0
CZ3 D:TRP659 4.4 31.4 1.0
CD2 D:TYR662 4.5 22.5 1.0
CG D:TYR631 4.6 24.6 1.0
N1 D:6Z8811 4.6 33.5 1.0
C24 D:6Z8811 4.6 36.2 1.0
CE2 D:TYR666 4.7 22.3 1.0
O12 D:6Z8811 4.7 26.4 1.0
CE1 D:TYR662 4.7 21.2 1.0
C D:SER630 4.8 31.9 1.0
CB D:SER630 4.8 27.5 1.0

Bromine binding site 8 out of 8 in 5lls

Go back to Bromine Binding Sites List in 5lls
Bromine binding site 8 out of 8 in the Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Porcine Dipeptidyl Peptidase IV in Complex with 8-(3-Aminopiperidin-1- Yl)-7-[(2-Bromophenyl)Methyl]-1,3-Dimethyl-2,3,6,7-Tetrahydro-1H- Purine-2,6-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br813

b:68.6
occ:0.62
 BR D:6Z8813 0.0 68.6 0.6
C15 D:6Z8813 1.9 60.9 0.6
C22 D:6Z8813 2.8 58.3 0.6
C9 D:6Z8813 2.9 54.9 0.6
C4 D:6Z8813 3.2 49.8 0.6
O D:ALA280 3.7 33.2 1.0
O D:PRO278 3.9 46.7 1.0
C D:ALA280 4.0 33.9 1.0
C D:ASN279 4.1 40.5 1.0
C28 D:6Z8813 4.1 55.8 0.6
N D:ALA280 4.1 33.1 1.0
C16 D:6Z8813 4.2 54.5 0.6
O D:ASN279 4.3 40.5 1.0
CA D:ASN279 4.4 39.7 1.0
N D:SER281 4.4 28.1 1.0
N1 D:6Z8813 4.5 45.7 0.6
CA D:ALA280 4.6 31.0 1.0
C13 D:6Z8813 4.6 46.3 0.6
C24 D:6Z8813 4.6 54.6 0.6
N8 D:6Z8813 4.7 45.7 0.6
CA D:SER281 4.8 25.4 1.0
C14 D:6Z8813 4.8 45.4 0.6
C D:PRO278 4.8 46.0 1.0

Reference:

G.Schnapp, T.Klein, Y.Hoevels, R.A.Bakker, H.Nar. Comparative Analysis of Binding Kinetics and Thermodynamics of Dipeptidyl Peptidase-4 Inhibitors and Their Relationship to Structure. J.Med.Chem. V. 59 7466 2016.
ISSN: ISSN 0022-2623
PubMed: 27438064
DOI: 10.1021/ACS.JMEDCHEM.6B00475
Page generated: Thu Jul 11 00:11:35 2024

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