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Fluorine in PDB 2oqi: Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine

Enzymatic activity of Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine

All present enzymatic activity of Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine:
3.4.14.5;

Protein crystallography data

The structure of Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine, PDB code: 2oqi was solved by Z.Pei, X.Li, T.W.Von Geldern, K.L.Longenecker, D.Pireh, K.D.Stewart, B.J.Backes, C.Lai, T.H.Lubben, S.J.Ballaron, D.W.Beno, A.J.Kempf-Grote, H.L.Sham, J.M.Trevillyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 119.294, 127.300, 126.799, 90.00, 96.45, 90.00
R / Rfree (%) 23.9 / 28.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine (pdb code 2oqi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine, PDB code: 2oqi:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2oqi

Go back to Fluorine Binding Sites List in 2oqi
Fluorine binding site 1 out of 3 in the Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:30.4
occ:1.00
F B:GGO901 0.0 30.4 1.0
C22 B:GGO901 1.3 30.4 1.0
C21 B:GGO901 2.3 30.4 1.0
C24 B:GGO901 2.4 30.4 1.0
F25 B:GGO901 2.8 30.4 1.0
CD2 B:TYR631 3.3 22.1 1.0
CB B:TYR631 3.6 22.1 1.0
OH B:TYR666 3.6 10.5 1.0
C20 B:GGO901 3.6 30.4 1.0
C26 B:GGO901 3.6 30.4 1.0
CZ B:TYR666 3.7 10.5 1.0
CE1 B:TYR666 3.7 10.5 1.0
CG B:TYR631 3.9 22.1 1.0
CA B:TYR631 4.0 14.5 1.0
C27 B:GGO901 4.1 30.4 1.0
N B:TYR631 4.1 14.5 1.0
CH2 B:TRP659 4.2 10.8 1.0
CE2 B:TYR631 4.3 22.1 1.0
CE2 B:TYR666 4.4 10.5 1.0
CE2 B:TYR662 4.4 19.6 1.0
CZ3 B:TRP659 4.4 10.8 1.0
CD1 B:TYR666 4.5 10.5 1.0
CG2 B:VAL656 4.7 11.2 1.0
CZ B:TYR662 4.7 19.6 1.0
OH B:TYR547 4.7 26.4 1.0
CD2 B:TYR662 4.8 19.6 1.0
C19 B:GGO901 4.9 30.4 1.0
OH B:TYR662 5.0 19.6 1.0

Fluorine binding site 2 out of 3 in 2oqi

Go back to Fluorine Binding Sites List in 2oqi
Fluorine binding site 2 out of 3 in the Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:30.4
occ:1.00
F25 B:GGO901 0.0 30.4 1.0
C24 B:GGO901 1.3 30.4 1.0
C26 B:GGO901 2.3 30.4 1.0
C22 B:GGO901 2.4 30.4 1.0
F B:GGO901 2.8 30.4 1.0
CG2 B:VAL711 3.2 21.3 1.0
CG2 B:VAL656 3.3 11.2 1.0
C27 B:GGO901 3.6 30.4 1.0
C21 B:GGO901 3.6 30.4 1.0
N B:TYR631 3.7 14.5 1.0
CB B:SER630 3.9 32.8 1.0
C B:SER630 3.9 18.3 1.0
CA B:SER630 4.0 18.3 1.0
C20 B:GGO901 4.1 30.4 1.0
CE1 B:TYR662 4.2 19.6 1.0
CZ B:TYR662 4.2 19.6 1.0
CA B:TYR631 4.4 14.5 1.0
NE2 B:HIS740 4.4 7.3 1.0
OH B:TYR662 4.5 19.6 1.0
CE1 B:HIS740 4.5 7.3 1.0
CB B:VAL711 4.6 21.3 1.0
CB B:VAL656 4.6 11.2 1.0
O B:SER630 4.6 18.3 1.0
CD1 B:TYR662 4.6 19.6 1.0
F28 B:GGO901 4.7 30.4 1.0
CE2 B:TYR662 4.7 19.6 1.0
CG1 B:VAL711 4.7 21.3 1.0
OG B:SER630 4.8 32.8 1.0
CB B:TYR631 4.8 22.1 1.0

Fluorine binding site 3 out of 3 in 2oqi

Go back to Fluorine Binding Sites List in 2oqi
Fluorine binding site 3 out of 3 in the Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-Constrained Phenethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:30.4
occ:1.00
F28 B:GGO901 0.0 30.4 1.0
C27 B:GGO901 1.3 30.4 1.0
C26 B:GGO901 2.3 30.4 1.0
C20 B:GGO901 2.4 30.4 1.0
C19 B:GGO901 2.9 30.4 1.0
N B:GGO901 3.0 30.4 1.0
NH2 B:ARG125 3.1 16.2 1.0
OE2 B:GLU205 3.3 15.7 1.0
ND2 B:ASN710 3.4 15.6 1.0
C B:GGO901 3.5 30.4 1.0
C24 B:GGO901 3.6 30.4 1.0
OH B:TYR662 3.6 19.6 1.0
C21 B:GGO901 3.7 30.4 1.0
CD2 B:HIS740 3.8 7.3 1.0
NE2 B:HIS740 3.8 7.3 1.0
OD1 B:ASN710 3.8 15.6 1.0
CG B:ASN710 3.8 15.6 1.0
C22 B:GGO901 4.1 30.4 1.0
C18 B:GGO901 4.2 30.4 1.0
CZ B:ARG125 4.4 16.2 1.0
C3 B:GGO901 4.5 30.4 1.0
CD B:GLU205 4.5 15.7 1.0
F25 B:GGO901 4.7 30.4 1.0
OG B:SER630 4.7 32.8 1.0
CZ B:TYR662 4.7 19.6 1.0
NH1 B:ARG125 4.9 16.2 1.0
CG B:HIS740 4.9 7.3 1.0
CE1 B:HIS740 4.9 7.3 1.0
CB B:ASN710 5.0 15.6 1.0

Reference:

Z.Pei, X.Li, T.W.Geldern, K.Longenecker, D.Pireh, K.D.Stewart, B.J.Backes, C.Lai, T.H.Lubben, S.J.Ballaron, D.W.Beno, A.J.Kempf-Grote, H.L.Sham, J.M.Trevillyan. Discovery and Structure-Activity Relationships of Piperidinone- and Piperidine-Constrained Phenethylamines As Novel, Potent, and Selective Dipeptidyl Peptidase IV Inhibitors. J.Med.Chem. V. 50 1983 2007.
ISSN: ISSN 0022-2623
PubMed: 17367123
DOI: 10.1021/JM061436D
Page generated: Wed Oct 28 14:46:57 2020

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