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Fluorine in PDB 5ism: Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor

Enzymatic activity of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor

All present enzymatic activity of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor:
3.4.14.5;

Protein crystallography data

The structure of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor, PDB code: 5ism was solved by G.Scapin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.274, 126.029, 137.273, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.1

Other elements in 5ism:

The structure of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor (pdb code 5ism). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor, PDB code: 5ism:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5ism

Go back to Fluorine Binding Sites List in 5ism
Fluorine binding site 1 out of 6 in the Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F811

b:15.3
occ:1.00
 F27 A:6DG811 0.0 15.3 1.0
C12 A:6DG811 1.3 14.2 1.0
C13 A:6DG811 2.3 14.5 1.0
C2 A:6DG811 2.3 14.4 1.0
C19 A:6DG811 2.7 14.7 1.0
ND2 A:ASN710 3.1 12.6 1.0
NH2 A:ARG125 3.3 16.9 1.0
OE2 A:GLU205 3.3 12.8 1.0
N20 A:6DG811 3.4 13.7 1.0
OH A:TYR662 3.5 11.7 1.0
OD1 A:ASN710 3.5 13.9 1.0
C3 A:6DG811 3.6 14.1 1.0
CG A:ASN710 3.6 12.6 1.0
C1 A:6DG811 3.6 14.9 1.0
O A:HOH1366 3.7 21.4 1.0
C18 A:6DG811 3.7 14.3 1.0
NE2 A:HIS740 3.7 13.9 1.0
CD2 A:HIS740 3.8 14.1 1.0
OG A:SER630 3.9 14.8 0.4
O A:HOH978 3.9 17.3 1.0
OG A:SER630 3.9 15.3 0.6
O25 A:6DG811 3.9 15.2 1.0
C11 A:6DG811 4.0 15.1 1.0
CD A:GLU205 4.5 13.6 1.0
CZ A:TYR662 4.6 11.5 1.0
O A:HOH1592 4.6 38.1 1.0
CZ A:ARG125 4.7 17.1 1.0
C6 A:6DG811 4.7 14.7 1.0
CE1 A:HIS740 4.8 14.0 1.0
C7 A:6DG811 4.8 15.4 1.0
CB A:ASN710 4.8 12.3 1.0
CG A:HIS740 4.8 13.7 1.0

Fluorine binding site 2 out of 6 in 5ism

Go back to Fluorine Binding Sites List in 5ism
Fluorine binding site 2 out of 6 in the Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F811

b:16.1
occ:1.00
 F26 A:6DG811 0.0 16.1 1.0
C11 A:6DG811 1.3 15.1 1.0
C1 A:6DG811 2.3 14.9 1.0
C3 A:6DG811 2.4 14.1 1.0
CD2 A:TYR631 3.5 12.9 1.0
C2 A:6DG811 3.6 14.4 1.0
C13 A:6DG811 3.6 14.5 1.0
CE1 A:TYR666 3.7 12.6 1.0
CH2 A:TRP659 3.8 11.7 1.0
CB A:TYR631 3.9 13.0 1.0
CG2 A:VAL656 3.9 11.8 1.0
CZ A:TYR666 3.9 13.0 1.0
OH A:TYR666 3.9 13.6 1.0
CZ3 A:TRP659 4.0 11.8 1.0
C12 A:6DG811 4.1 14.2 1.0
CA A:TYR631 4.1 12.7 1.0
N A:TYR631 4.1 12.6 1.0
CG A:TYR631 4.1 12.8 1.0
CE2 A:TYR662 4.2 11.6 1.0
CD1 A:TYR666 4.4 12.6 1.0
CZ A:TYR662 4.4 11.5 1.0
CE2 A:TYR631 4.5 13.3 1.0
CD2 A:TYR662 4.5 11.7 1.0
OG A:SER630 4.6 15.3 0.6
OG A:SER630 4.6 14.8 0.4
OH A:TYR662 4.7 11.7 1.0
CE2 A:TYR666 4.8 13.3 1.0
C19 A:6DG811 4.9 14.7 1.0
CB A:VAL656 4.9 11.5 1.0
CE1 A:TYR662 4.9 11.7 1.0
CZ2 A:TRP659 5.0 12.0 1.0
C A:SER630 5.0 13.1 1.0

Fluorine binding site 3 out of 6 in 5ism

Go back to Fluorine Binding Sites List in 5ism
Fluorine binding site 3 out of 6 in the Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F810

b:18.1
occ:0.60
 F27 B:6DG810 0.0 18.1 0.6
F27 B:6DG810 0.6 9.7 0.4
C12 B:6DG810 1.3 9.8 0.4
C12 B:6DG810 1.3 18.7 0.6
C13 B:6DG810 2.2 9.6 0.4
C2 B:6DG810 2.3 9.8 0.4
C2 B:6DG810 2.4 18.5 0.6
C13 B:6DG810 2.4 18.9 0.6
C19 B:6DG810 2.8 9.4 0.4
C19 B:6DG810 2.8 19.5 0.6
NH2 B:ARG125 3.3 18.8 1.0
ND2 B:ASN710 3.4 13.0 1.0
C3 B:6DG810 3.5 9.8 0.4
C1 B:6DG810 3.5 10.0 0.4
O B:HOH1010 3.5 22.8 1.0
O B:HOH1431 3.5 25.9 1.0
NE2 B:HIS740 3.6 14.9 1.0
OE2 B:GLU205 3.6 16.5 1.0
CD2 B:HIS740 3.6 14.5 1.0
OD1 B:ASN710 3.6 13.0 1.0
OG B:SER630 3.6 15.9 1.0
C1 B:6DG810 3.6 18.3 0.6
C3 B:6DG810 3.6 18.2 0.6
N20 B:6DG810 3.7 19.3 0.6
OH B:TYR662 3.7 13.0 1.0
N20 B:6DG810 3.7 9.2 0.4
CG B:ASN710 3.7 12.7 1.0
O25 B:6DG810 3.8 9.5 0.4
C18 B:6DG810 3.9 9.3 0.4
O25 B:6DG810 3.9 20.6 0.6
C18 B:6DG810 3.9 19.9 0.6
C11 B:6DG810 3.9 10.0 0.4
C11 B:6DG810 4.1 18.4 0.6
CZ B:ARG125 4.6 19.9 1.0
C7 B:6DG810 4.6 9.3 0.4
CE1 B:HIS740 4.6 14.8 1.0
CG B:HIS740 4.7 14.3 1.0
CD B:GLU205 4.7 15.5 1.0
C7 B:6DG810 4.8 21.2 0.6
CZ B:TYR662 4.8 12.8 1.0
CB B:SER630 4.8 14.8 1.0
C6 B:6DG810 4.9 9.3 0.4
CB B:ASN710 4.9 12.7 1.0
C6 B:6DG810 4.9 20.9 0.6

Fluorine binding site 4 out of 6 in 5ism

Go back to Fluorine Binding Sites List in 5ism
Fluorine binding site 4 out of 6 in the Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F810

b:9.7
occ:0.40
 F27 B:6DG810 0.0 9.7 0.4
F27 B:6DG810 0.6 18.1 0.6
C12 B:6DG810 1.3 9.8 0.4
C12 B:6DG810 1.5 18.7 0.6
C2 B:6DG810 2.3 9.8 0.4
C13 B:6DG810 2.4 9.6 0.4
C2 B:6DG810 2.5 18.5 0.6
C13 B:6DG810 2.5 18.9 0.6
C19 B:6DG810 2.8 9.4 0.4
C19 B:6DG810 2.9 19.5 0.6
ND2 B:ASN710 2.9 13.0 1.0
OE2 B:GLU205 3.2 16.5 1.0
OD1 B:ASN710 3.2 13.0 1.0
NH2 B:ARG125 3.2 18.8 1.0
OH B:TYR662 3.3 13.0 1.0
CG B:ASN710 3.3 12.7 1.0
N20 B:6DG810 3.4 19.3 0.6
N20 B:6DG810 3.4 9.2 0.4
C1 B:6DG810 3.6 10.0 0.4
C3 B:6DG810 3.6 9.8 0.4
C1 B:6DG810 3.7 18.3 0.6
C3 B:6DG810 3.7 18.2 0.6
C18 B:6DG810 3.8 9.3 0.4
C18 B:6DG810 3.8 19.9 0.6
CD2 B:HIS740 3.8 14.5 1.0
NE2 B:HIS740 3.9 14.9 1.0
O B:HOH1431 3.9 25.9 1.0
O25 B:6DG810 4.0 9.5 0.4
O B:HOH1010 4.0 22.8 1.0
C11 B:6DG810 4.1 10.0 0.4
OG B:SER630 4.1 15.9 1.0
O25 B:6DG810 4.1 20.6 0.6
C11 B:6DG810 4.2 18.4 0.6
CD B:GLU205 4.3 15.5 1.0
CZ B:TYR662 4.4 12.8 1.0
CZ B:ARG125 4.6 19.9 1.0
CB B:ASN710 4.6 12.7 1.0
C6 B:6DG810 4.7 9.3 0.4
C7 B:6DG810 4.8 9.3 0.4
C6 B:6DG810 4.8 20.9 0.6
CG B:HIS740 4.8 14.3 1.0
CE1 B:HIS740 4.9 14.8 1.0
C7 B:6DG810 4.9 21.2 0.6
CE1 B:TYR662 5.0 12.6 1.0

Fluorine binding site 5 out of 6 in 5ism

Go back to Fluorine Binding Sites List in 5ism
Fluorine binding site 5 out of 6 in the Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F810

b:18.2
occ:0.60
 F26 B:6DG810 0.0 18.2 0.6
F26 B:6DG810 0.7 10.6 0.4
C11 B:6DG810 1.4 18.4 0.6
C11 B:6DG810 1.6 10.0 0.4
C3 B:6DG810 2.4 18.2 0.6
C1 B:6DG810 2.4 18.3 0.6
C3 B:6DG810 2.5 9.8 0.4
C1 B:6DG810 2.6 10.0 0.4
CE1 B:TYR666 3.4 15.2 1.0
CH2 B:TRP659 3.6 14.0 1.0
CD2 B:TYR631 3.6 14.3 1.0
C2 B:6DG810 3.7 18.5 0.6
C13 B:6DG810 3.7 18.9 0.6
CZ B:TYR666 3.7 14.8 1.0
C13 B:6DG810 3.8 9.6 0.4
C2 B:6DG810 3.8 9.8 0.4
CZ3 B:TRP659 3.8 13.9 1.0
OH B:TYR666 3.9 15.9 1.0
CG2 B:VAL656 3.9 13.6 1.0
CE2 B:TYR662 3.9 12.4 1.0
CD1 B:TYR666 4.0 14.5 1.0
CB B:TYR631 4.1 14.5 1.0
C12 B:6DG810 4.1 18.7 0.6
CD2 B:TYR662 4.2 12.6 1.0
C12 B:6DG810 4.3 9.8 0.4
CZ B:TYR662 4.3 12.8 1.0
CG B:TYR631 4.3 14.4 1.0
CA B:TYR631 4.4 14.2 1.0
N B:TYR631 4.5 13.5 1.0
CE2 B:TYR631 4.5 14.6 1.0
CE2 B:TYR666 4.6 14.5 1.0
OH B:TYR662 4.7 13.0 1.0
CG B:TYR662 4.8 12.6 1.0
CE1 B:TYR662 4.8 12.6 1.0
CZ2 B:TRP659 4.9 14.3 1.0
CG B:TYR666 4.9 14.2 1.0
C19 B:6DG810 4.9 19.5 0.6
OG B:SER630 4.9 15.9 1.0
C19 B:6DG810 5.0 9.4 0.4

Fluorine binding site 6 out of 6 in 5ism

Go back to Fluorine Binding Sites List in 5ism
Fluorine binding site 6 out of 6 in the Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F810

b:10.6
occ:0.40
 F26 B:6DG810 0.0 10.6 0.4
F26 B:6DG810 0.7 18.2 0.6
C11 B:6DG810 1.3 18.4 0.6
C11 B:6DG810 1.3 10.0 0.4
C1 B:6DG810 2.2 18.3 0.6
C3 B:6DG810 2.3 18.2 0.6
C1 B:6DG810 2.4 10.0 0.4
C3 B:6DG810 2.4 9.8 0.4
CD2 B:TYR631 3.4 14.3 1.0
C2 B:6DG810 3.5 18.5 0.6
C13 B:6DG810 3.5 18.9 0.6
CB B:TYR631 3.6 14.5 1.0
C2 B:6DG810 3.6 9.8 0.4
C13 B:6DG810 3.6 9.6 0.4
CA B:TYR631 3.8 14.2 1.0
N B:TYR631 3.8 13.5 1.0
CE1 B:TYR666 3.9 15.2 1.0
CH2 B:TRP659 3.9 14.0 1.0
CG B:TYR631 4.0 14.4 1.0
CG2 B:VAL656 4.0 13.6 1.0
C12 B:6DG810 4.0 18.7 0.6
OH B:TYR666 4.0 15.9 1.0
CZ B:TYR666 4.1 14.8 1.0
C12 B:6DG810 4.1 9.8 0.4
CZ3 B:TRP659 4.3 13.9 1.0
OG B:SER630 4.4 15.9 1.0
CE2 B:TYR662 4.5 12.4 1.0
CE2 B:TYR631 4.5 14.6 1.0
CD1 B:TYR666 4.6 14.5 1.0
CZ B:TYR662 4.7 12.8 1.0
C B:SER630 4.7 14.0 1.0
CD2 B:TYR662 4.8 12.6 1.0
C19 B:6DG810 4.8 19.5 0.6
OH B:TYR547 4.9 21.6 1.0
C19 B:6DG810 4.9 9.4 0.4
O25 B:6DG810 4.9 20.6 0.6
CE2 B:TYR666 4.9 14.5 1.0
OH B:TYR662 5.0 13.0 1.0

Reference:

J.M.Cox, H.D.Chu, J.T.Kuethe, Y.D.Gao, G.Scapin, G.Eiermann, H.He, X.Li, K.A.Lyons, J.Metzger, A.Petrov, J.K.Wu, S.Xu, R.Sinha-Roy, A.E.Weber, T.Biftu. The Discovery of Novel 5,6,5- and 5,5,6-Tricyclic Pyrrolidines As Potent and Selective Dpp-4 Inhibitors. Bioorg.Med.Chem.Lett. V. 26 2622 2016.
ISSN: ESSN 1464-3405
PubMed: 27106708
DOI: 10.1016/J.BMCL.2016.04.020
Page generated: Thu Aug 1 10:16:20 2024

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