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Fluorine in PDB 3d4l: Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor

Enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor

All present enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor:
3.4.14.5;

Protein crystallography data

The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor, PDB code: 3d4l was solved by G.Scapin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.435, 125.749, 137.175, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3d4l:

The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor (pdb code 3d4l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor, PDB code: 3d4l:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3d4l

Go back to Fluorine Binding Sites List in 3d4l
Fluorine binding site 1 out of 4 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor


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/CD26 in Complex with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1521

b:25.3
occ:1.00
F34 A:6051521 0.0 25.3 1.0
C5 A:6051521 1.3 24.7 1.0
C6 A:6051521 2.4 23.8 1.0
C4 A:6051521 2.4 22.5 1.0
CD2 A:TYR631 3.5 22.6 1.0
CH2 A:TRP659 3.6 20.5 1.0
C1 A:6051521 3.7 22.9 1.0
C3 A:6051521 3.7 22.4 1.0
CE1 A:TYR666 3.7 20.5 1.0
CB A:TYR631 3.8 21.4 1.0
CG2 A:VAL656 3.8 19.6 1.0
OH A:TYR666 3.9 22.7 1.0
CZ3 A:TRP659 3.9 19.9 1.0
CZ A:TYR666 3.9 21.9 1.0
CA A:TYR631 4.1 21.5 1.0
CG A:TYR631 4.1 22.2 1.0
C2 A:6051521 4.2 22.4 1.0
CE2 A:TYR662 4.2 20.5 1.0
N A:TYR631 4.2 21.1 1.0
CE2 A:TYR631 4.5 23.7 1.0
CZ A:TYR662 4.5 20.8 1.0
CD2 A:TYR662 4.5 20.0 1.0
CD1 A:TYR666 4.5 21.2 1.0
OG A:SER630 4.7 26.1 1.0
OH A:TYR662 4.8 21.2 1.0
CE2 A:TYR666 4.8 22.4 1.0
CB A:VAL656 4.9 21.4 1.0
CZ2 A:TRP659 4.9 20.8 1.0
C10 A:6051521 4.9 22.0 1.0
CE1 A:TYR662 4.9 21.0 1.0
CG A:TYR662 5.0 21.2 1.0

Fluorine binding site 2 out of 4 in 3d4l

Go back to Fluorine Binding Sites List in 3d4l
Fluorine binding site 2 out of 4 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor


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/CD26 in Complex with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1521

b:23.1
occ:1.00
F35 A:6051521 0.0 23.1 1.0
C2 A:6051521 1.3 22.4 1.0
C1 A:6051521 2.3 22.9 1.0
C3 A:6051521 2.4 22.4 1.0
C10 A:6051521 2.9 22.0 1.0
ND2 A:ASN710 3.1 21.3 1.0
NH2 A:ARG125 3.2 24.0 1.0
OE2 A:GLU205 3.3 21.7 1.0
N15 A:6051521 3.4 17.7 1.0
O A:HOH1574 3.6 27.8 1.0
OH A:TYR662 3.6 21.2 1.0
OD1 A:ASN710 3.6 22.6 1.0
CG A:ASN710 3.6 22.4 1.0
C6 A:6051521 3.6 23.8 1.0
C4 A:6051521 3.7 22.5 1.0
NE2 A:HIS740 3.8 25.1 1.0
O A:HOH1710 3.8 38.5 1.0
C11 A:6051521 3.8 20.2 1.0
CD2 A:HIS740 3.8 25.7 1.0
OG A:SER630 3.8 26.1 1.0
C5 A:6051521 4.1 24.7 1.0
CD A:GLU205 4.5 22.9 1.0
CZ A:ARG125 4.5 25.1 1.0
CZ A:TYR662 4.7 20.8 1.0
CB A:ASN710 4.8 21.9 1.0
CE1 A:HIS740 4.8 26.1 1.0
C14 A:6051521 4.8 20.6 1.0
CG A:HIS740 4.8 25.5 1.0

Fluorine binding site 3 out of 4 in 3d4l

Go back to Fluorine Binding Sites List in 3d4l
Fluorine binding site 3 out of 4 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor


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/CD26 in Complex with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1521

b:25.1
occ:1.00
F34 B:6051521 0.0 25.1 1.0
C5 B:6051521 1.3 23.9 1.0
C4 B:6051521 2.3 23.3 1.0
C6 B:6051521 2.4 22.1 1.0
CD2 B:TYR631 3.5 24.3 1.0
C3 B:6051521 3.7 23.4 1.0
C1 B:6051521 3.7 22.4 1.0
CH2 B:TRP659 3.8 23.9 1.0
CG2 B:VAL656 3.8 21.1 1.0
CE1 B:TYR666 3.8 23.9 1.0
CB B:TYR631 3.8 23.4 1.0
OH B:TYR666 4.0 24.2 1.0
CZ B:TYR666 4.0 24.4 1.0
CA B:TYR631 4.1 24.1 1.0
CZ3 B:TRP659 4.1 23.2 1.0
CG B:TYR631 4.1 23.6 1.0
C2 B:6051521 4.1 23.1 1.0
CE2 B:TYR662 4.2 21.2 1.0
N B:TYR631 4.2 24.4 1.0
CZ B:TYR662 4.4 23.0 1.0
CE2 B:TYR631 4.5 24.1 1.0
CD1 B:TYR666 4.5 24.2 1.0
CD2 B:TYR662 4.5 20.7 1.0
OG B:SER630 4.6 27.7 1.0
CB B:VAL656 4.8 22.0 1.0
OH B:TYR662 4.8 22.8 1.0
CE2 B:TYR666 4.9 23.9 1.0
C10 B:6051521 4.9 23.4 1.0
CE1 B:TYR662 4.9 22.9 1.0
CZ2 B:TRP659 5.0 24.1 1.0

Fluorine binding site 4 out of 4 in 3d4l

Go back to Fluorine Binding Sites List in 3d4l
Fluorine binding site 4 out of 4 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Dipeptidyl Peptidase IV/CD26 in Complex with A Novel Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1521

b:23.8
occ:1.00
F35 B:6051521 0.0 23.8 1.0
C2 B:6051521 1.3 23.1 1.0
C3 B:6051521 2.4 23.4 1.0
C1 B:6051521 2.4 22.4 1.0
C10 B:6051521 2.9 23.4 1.0
NH2 B:ARG125 3.0 25.2 1.0
ND2 B:ASN710 3.3 21.9 1.0
OE2 B:GLU205 3.3 25.2 1.0
N15 B:6051521 3.4 22.0 1.0
OD1 B:ASN710 3.5 20.0 1.0
OH B:TYR662 3.6 22.8 1.0
O B:HOH2456 3.6 29.5 1.0
CG B:ASN710 3.6 22.5 1.0
C6 B:6051521 3.7 22.1 1.0
C4 B:6051521 3.7 23.3 1.0
CD2 B:HIS740 3.8 22.1 1.0
O B:HOH2556 3.8 40.5 1.0
C11 B:6051521 3.8 23.5 1.0
NE2 B:HIS740 3.8 22.1 1.0
OG B:SER630 3.9 27.7 1.0
C5 B:6051521 4.1 23.9 1.0
CZ B:ARG125 4.4 24.7 1.0
CD B:GLU205 4.5 24.4 1.0
CZ B:TYR662 4.7 23.0 1.0
C14 B:6051521 4.8 24.9 1.0
CG B:HIS740 4.9 22.6 1.0
CE1 B:HIS740 4.9 22.6 1.0
CB B:ASN710 4.9 22.3 1.0

Reference:

G.B.Liang, X.Qian, T.Biftu, S.Singh, Y.D.Gao, G.Scapin, S.Patel, B.Leiting, R.Patel, J.Wu, X.Zhang, N.A.Thornberry, A.E.Weber. Discovery of New Binding Elements in Dpp-4 Inhibition and Their Applications in Novel Dpp-4 Inhibitor Design. Bioorg.Med.Chem.Lett. V. 18 3706 2008.
ISSN: ISSN 0960-894X
PubMed: 18524582
DOI: 10.1016/J.BMCL.2008.05.061
Page generated: Wed Jul 31 17:51:31 2024

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