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Bromine in PDB 4g1f: Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue

Enzymatic activity of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue

All present enzymatic activity of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue:
3.4.14.5;

Protein crystallography data

The structure of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue, PDB code: 4g1f was solved by R.J.Skene, S.L.Gwaltney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 121.622, 121.362, 143.257, 90.00, 114.63, 90.00
R / Rfree (%) 20.7 / 25.9

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue (pdb code 4g1f). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue, PDB code: 4g1f:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 4g1f

Go back to Bromine Binding Sites List in 4g1f
Bromine binding site 1 out of 4 in the Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br800

b:39.4
occ:1.00
BR1 A:0WG800 0.0 39.4 1.0
C16 A:0WG800 1.9 32.8 1.0
C15 A:0WG800 2.8 31.9 1.0
C11 A:0WG800 2.9 31.5 1.0
C10 A:0WG800 3.1 30.1 1.0
O A:HOH955 3.3 31.4 1.0
C18 A:0WG800 3.5 29.0 1.0
OD1 A:ASN710 3.6 19.5 1.0
NH2 A:ARG125 3.6 27.9 1.0
NE2 A:HIS740 3.6 22.1 1.0
O20 A:0WG800 3.7 26.0 1.0
C7 A:0WG800 3.7 29.9 1.0
N9 A:0WG800 3.8 26.1 1.0
C19 A:0WG800 3.8 27.6 1.0
CD2 A:HIS740 3.8 21.6 1.0
CB A:SER630 3.9 19.6 1.0
OH A:TYR662 4.0 20.9 1.0
OG A:SER630 4.0 19.6 1.0
C14 A:0WG800 4.1 30.1 1.0
OE1 A:GLU205 4.2 24.0 1.0
O A:HOH956 4.2 37.9 1.0
C12 A:0WG800 4.2 30.9 1.0
C8 A:0WG800 4.2 28.1 1.0
CG A:ASN710 4.4 19.3 1.0
C3 A:0WG800 4.4 29.9 1.0
C5 A:0WG800 4.6 30.9 1.0
C13 A:0WG800 4.7 30.8 1.0
ND2 A:ASN710 4.7 19.8 1.0
N21 A:0WG800 4.8 28.0 1.0
CE1 A:HIS740 4.8 22.4 1.0
N4 A:0WG800 4.8 30.7 1.0
CZ A:ARG125 4.9 28.6 1.0

Bromine binding site 2 out of 4 in 4g1f

Go back to Bromine Binding Sites List in 4g1f
Bromine binding site 2 out of 4 in the Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br800

b:46.9
occ:1.00
BR1 B:0WG800 0.0 46.9 1.0
C16 B:0WG800 1.9 36.5 1.0
C15 B:0WG800 2.8 35.1 1.0
C11 B:0WG800 2.9 34.5 1.0
O B:HOH958 3.1 30.4 1.0
C10 B:0WG800 3.1 32.2 1.0
NE2 B:HIS740 3.5 21.7 1.0
C18 B:0WG800 3.5 32.0 1.0
N9 B:0WG800 3.7 26.8 1.0
O20 B:0WG800 3.7 31.9 1.0
CD2 B:HIS740 3.7 21.6 1.0
C7 B:0WG800 3.8 30.7 1.0
NH2 B:ARG125 3.8 30.7 1.0
OG B:SER630 3.8 21.6 1.0
CB B:SER630 3.8 22.4 1.0
C19 B:0WG800 3.8 32.0 1.0
OH B:TYR662 4.0 27.1 1.0
OD1 B:ASN710 4.0 20.1 1.0
C14 B:0WG800 4.1 34.3 1.0
OE1 B:GLU205 4.2 29.6 1.0
C12 B:0WG800 4.2 33.8 1.0
C8 B:0WG800 4.2 28.7 1.0
ND2 B:ASN710 4.3 21.2 1.0
CG B:ASN710 4.4 20.4 1.0
C3 B:0WG800 4.5 32.1 1.0
CE1 B:HIS740 4.5 21.8 1.0
C5 B:0WG800 4.6 31.6 1.0
C13 B:0WG800 4.7 33.5 1.0
N21 B:0WG800 4.8 32.7 1.0
N4 B:0WG800 4.9 32.3 1.0
CG B:HIS740 4.9 21.5 1.0

Bromine binding site 3 out of 4 in 4g1f

Go back to Bromine Binding Sites List in 4g1f
Bromine binding site 3 out of 4 in the Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br800

b:41.2
occ:1.00
BR1 C:0WG800 0.0 41.2 1.0
C16 C:0WG800 1.9 32.5 1.0
C15 C:0WG800 2.8 32.1 1.0
C11 C:0WG800 2.9 31.3 1.0
C10 C:0WG800 3.1 30.7 1.0
O C:HOH902 3.3 13.7 1.0
NH2 C:ARG125 3.5 27.0 1.0
NE2 C:HIS740 3.5 25.6 1.0
C18 C:0WG800 3.6 30.7 1.0
OD1 C:ASN710 3.6 21.4 1.0
N9 C:0WG800 3.7 26.5 1.0
O20 C:0WG800 3.7 31.1 1.0
C7 C:0WG800 3.8 30.0 1.0
CD2 C:HIS740 3.8 25.4 1.0
C19 C:0WG800 3.9 31.2 1.0
OG C:SER630 3.9 21.8 1.0
CB C:SER630 4.0 21.7 1.0
OH C:TYR662 4.0 23.9 1.0
OE1 C:GLU205 4.1 31.5 1.0
C14 C:0WG800 4.2 31.4 1.0
C12 C:0WG800 4.2 30.2 1.0
C8 C:0WG800 4.2 28.1 1.0
CG C:ASN710 4.4 20.9 1.0
C3 C:0WG800 4.5 30.7 1.0
CE1 C:HIS740 4.6 25.4 1.0
C5 C:0WG800 4.6 30.4 1.0
CZ C:ARG125 4.6 27.7 1.0
C13 C:0WG800 4.7 30.5 1.0
ND2 C:ASN710 4.7 20.2 1.0
N21 C:0WG800 4.9 31.3 1.0
N4 C:0WG800 4.9 30.5 1.0
CG C:HIS740 5.0 25.5 1.0

Bromine binding site 4 out of 4 in 4g1f

Go back to Bromine Binding Sites List in 4g1f
Bromine binding site 4 out of 4 in the Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Human Dipeptidyl Peptidase IV in Complex with A Pyridopyrimidinedione Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br800

b:45.5
occ:1.00
BR1 D:0WG800 0.0 45.5 1.0
C16 D:0WG800 1.9 36.4 1.0
C15 D:0WG800 2.8 34.7 1.0
C11 D:0WG800 2.9 34.6 1.0
O D:HOH901 3.0 15.9 1.0
C10 D:0WG800 3.1 32.4 1.0
C18 D:0WG800 3.6 31.5 1.0
NE2 D:HIS740 3.6 23.8 1.0
C7 D:0WG800 3.7 31.4 1.0
NH2 D:ARG125 3.7 24.8 1.0
O20 D:0WG800 3.8 30.8 1.0
CD2 D:HIS740 3.8 23.4 1.0
N9 D:0WG800 3.8 29.6 1.0
OG D:SER630 3.8 26.1 1.0
CB D:SER630 3.9 26.0 1.0
C19 D:0WG800 3.9 30.9 1.0
OH D:TYR662 3.9 25.3 1.0
C14 D:0WG800 4.1 34.6 1.0
OD1 D:ASN710 4.1 25.3 1.0
C8 D:0WG800 4.1 30.1 1.0
C12 D:0WG800 4.2 34.5 1.0
ND2 D:ASN710 4.2 24.7 1.0
OE1 D:GLU205 4.3 25.0 1.0
CG D:ASN710 4.3 24.6 1.0
C3 D:0WG800 4.5 31.6 1.0
C5 D:0WG800 4.6 31.5 1.0
C13 D:0WG800 4.7 35.1 1.0
CE1 D:HIS740 4.7 23.5 1.0
CG D:HIS740 4.9 23.3 1.0
N4 D:0WG800 4.9 31.8 1.0
N21 D:0WG800 4.9 30.7 1.0
CZ D:TYR662 4.9 25.1 1.0
CZ D:ARG125 5.0 25.0 1.0

Reference:

B.Lam, Z.Zhang, J.A.Stafford, R.J.Skene, L.Shi, S.L.Gwaltney. Structure-Based Design of Pyridopyrimidinediones As Dipeptidyl Peptidase IV Inhibitors. Bioorg.Med.Chem.Lett. V. 22 6628 2012.
ISSN: ISSN 0960-894X
PubMed: 23025999
DOI: 10.1016/J.BMCL.2012.08.110
Page generated: Wed Jul 10 21:16:16 2024

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