Atomistry » Fluorine » PDB 4pb2-4q0d » 4pnz
Atomistry »
  Fluorine »
    PDB 4pb2-4q0d »
      4pnz »

Fluorine in PDB 4pnz: Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)

Enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)

All present enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102):
3.4.14.5;

Protein crystallography data

The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102), PDB code: 4pnz was solved by G.Scapin, Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.15 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.940, 125.777, 137.085, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.7

Other elements in 4pnz:

The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) 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 the Long-Acting Inhibitor Omarigliptin (Mk-3102) (pdb code 4pnz). 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 Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102), PDB code: 4pnz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4pnz

Go back to Fluorine Binding Sites List in 4pnz
Fluorine binding site 1 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


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 the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:22.3
occ:1.00
 F2 A:2VH802 0.0 22.3 1.0
C A:2VH802 1.4 21.4 1.0
C5 A:2VH802 2.3 20.8 1.0
C1 A:2VH802 2.4 18.0 1.0
F A:2VH802 2.7 22.0 1.0
CG2 A:VAL656 3.1 14.0 1.0
CG2 A:VAL711 3.2 14.6 1.0
OG A:SER630 3.4 26.2 1.0
C2 A:2VH802 3.6 17.7 1.0
C4 A:2VH802 3.6 18.1 1.0
N A:TYR631 3.8 13.0 1.0
C A:SER630 4.0 16.5 1.0
CE1 A:TYR662 4.1 14.8 1.0
C3 A:2VH802 4.1 19.4 1.0
CZ A:TYR662 4.2 16.0 1.0
CB A:VAL656 4.3 14.8 1.0
CA A:SER630 4.3 13.5 1.0
CB A:SER630 4.4 17.3 1.0
CA A:TYR631 4.4 13.5 1.0
OH A:TYR662 4.4 16.0 1.0
CD1 A:TYR662 4.5 15.9 1.0
O A:SER630 4.5 16.6 1.0
CB A:VAL711 4.6 14.7 1.0
CE2 A:TYR662 4.6 15.0 1.0
NE2 A:HIS740 4.7 17.7 1.0
F1 A:2VH802 4.7 18.6 1.0
N A:VAL656 4.8 12.1 1.0
CE1 A:HIS740 4.8 17.5 1.0
CG A:TYR662 4.9 14.4 1.0
CG1 A:VAL711 4.9 13.7 1.0
CB A:TYR631 4.9 14.0 1.0
CD2 A:TYR662 4.9 14.7 1.0

Fluorine binding site 2 out of 6 in 4pnz

Go back to Fluorine Binding Sites List in 4pnz
Fluorine binding site 2 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


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 the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:22.0
occ:1.00
 F A:2VH802 0.0 22.0 1.0
C5 A:2VH802 1.4 20.8 1.0
C A:2VH802 2.3 21.4 1.0
C4 A:2VH802 2.4 18.1 1.0
F2 A:2VH802 2.7 22.3 1.0
CD2 A:TYR631 3.4 14.3 1.0
CE1 A:TYR666 3.5 16.5 1.0
OH A:TYR666 3.6 17.2 1.0
C1 A:2VH802 3.6 18.0 1.0
C3 A:2VH802 3.6 19.4 1.0
CB A:TYR631 3.7 14.0 1.0
CZ A:TYR666 3.7 18.7 1.0
CH2 A:TRP659 3.9 16.2 1.0
CG A:TYR631 4.0 15.0 1.0
CA A:TYR631 4.0 13.5 1.0
C2 A:2VH802 4.0 17.7 1.0
N A:TYR631 4.1 13.0 1.0
CZ3 A:TRP659 4.3 15.8 1.0
CE2 A:TYR662 4.3 15.0 1.0
CD1 A:TYR666 4.3 16.8 1.0
CG2 A:VAL656 4.4 14.0 1.0
CE2 A:TYR631 4.4 15.7 1.0
OG A:SER630 4.6 26.2 1.0
CE2 A:TYR666 4.6 15.8 1.0
CZ A:TYR662 4.6 16.0 1.0
OH A:TYR547 4.7 25.5 1.0
CD2 A:TYR662 4.7 14.7 1.0
O A:HOH1082 4.8 28.1 1.0
OH A:TYR662 4.9 16.0 1.0
C6 A:2VH802 4.9 19.4 1.0
C A:SER630 5.0 16.5 1.0

Fluorine binding site 3 out of 6 in 4pnz

Go back to Fluorine Binding Sites List in 4pnz
Fluorine binding site 3 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


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 the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:18.6
occ:1.00
 F1 A:2VH802 0.0 18.6 1.0
C2 A:2VH802 1.3 17.7 1.0
C1 A:2VH802 2.3 18.0 1.0
C3 A:2VH802 2.3 19.4 1.0
C6 A:2VH802 2.8 19.4 1.0
NH2 A:ARG125 3.1 19.2 1.0
ND2 A:ASN710 3.2 14.9 1.0
OE2 A:GLU205 3.4 16.2 1.0
N A:2VH802 3.5 16.9 1.0
OH A:TYR662 3.5 16.0 1.0
O A:HOH1101 3.6 30.5 1.0
C A:2VH802 3.6 21.4 1.0
C4 A:2VH802 3.6 18.1 1.0
OD1 A:ASN710 3.6 17.8 1.0
CG A:ASN710 3.7 19.1 1.0
O A:HOH978 3.7 24.7 1.0
C10 A:2VH802 3.7 17.4 1.0
CD2 A:HIS740 3.8 18.7 1.0
NE2 A:HIS740 3.8 17.7 1.0
OG A:SER630 3.9 26.2 1.0
O A:2VH802 3.9 22.3 1.0
C5 A:2VH802 4.0 20.8 1.0
CZ A:ARG125 4.5 30.8 1.0
CD A:GLU205 4.6 22.5 1.0
F2 A:2VH802 4.7 22.3 1.0
CZ A:TYR662 4.7 16.0 1.0
C9 A:2VH802 4.8 19.5 1.0
C7 A:2VH802 4.8 18.9 1.0
CG A:HIS740 4.8 16.3 1.0
CE1 A:HIS740 4.9 17.5 1.0
CB A:ASN710 4.9 11.4 1.0

Fluorine binding site 4 out of 6 in 4pnz

Go back to Fluorine Binding Sites List in 4pnz
Fluorine binding site 4 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


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 the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:21.5
occ:1.00
 F2 B:2VH801 0.0 21.5 1.0
C B:2VH801 1.3 21.6 1.0
C5 B:2VH801 2.3 23.3 1.0
C1 B:2VH801 2.4 19.6 1.0
F B:2VH801 2.7 21.1 1.0
CG2 B:VAL656 3.0 15.6 1.0
CG2 B:VAL711 3.1 14.2 1.0
OG B:SER630 3.4 28.2 1.0
C2 B:2VH801 3.6 21.6 1.0
C4 B:2VH801 3.6 22.4 1.0
N B:TYR631 3.9 17.3 1.0
C B:SER630 4.1 20.2 1.0
CZ B:TYR662 4.1 16.7 1.0
CE1 B:TYR662 4.1 15.1 1.0
C3 B:2VH801 4.1 20.9 1.0
CB B:VAL656 4.3 16.1 1.0
CA B:SER630 4.4 17.8 1.0
OH B:TYR662 4.4 17.3 1.0
CB B:SER630 4.4 19.6 1.0
CD1 B:TYR662 4.5 15.8 1.0
CA B:TYR631 4.5 16.3 1.0
CE2 B:TYR662 4.5 16.4 1.0
CB B:VAL711 4.6 14.3 1.0
O B:SER630 4.6 18.3 1.0
NE2 B:HIS740 4.7 18.9 1.0
F1 B:2VH801 4.7 20.1 1.0
CE1 B:HIS740 4.8 18.8 1.0
N B:VAL656 4.8 14.6 1.0
CG B:TYR662 4.9 14.4 1.0
CD2 B:TYR662 4.9 15.7 1.0
CG1 B:VAL711 5.0 13.2 1.0
CB B:TYR631 5.0 16.3 1.0

Fluorine binding site 5 out of 6 in 4pnz

Go back to Fluorine Binding Sites List in 4pnz
Fluorine binding site 5 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:21.1
occ:1.00
 F B:2VH801 0.0 21.1 1.0
C5 B:2VH801 1.3 23.3 1.0
C B:2VH801 2.3 21.6 1.0
C4 B:2VH801 2.3 22.4 1.0
F2 B:2VH801 2.7 21.5 1.0
CD2 B:TYR631 3.3 16.6 1.0
OH B:TYR666 3.5 23.2 1.0
CE1 B:TYR666 3.6 21.1 1.0
C1 B:2VH801 3.6 19.6 1.0
C3 B:2VH801 3.6 20.9 1.0
CZ B:TYR666 3.7 22.5 1.0
CB B:TYR631 3.7 16.3 1.0
CG B:TYR631 4.0 16.5 1.0
CH2 B:TRP659 4.0 17.5 1.0
C2 B:2VH801 4.0 21.6 1.0
CA B:TYR631 4.1 16.3 1.0
N B:TYR631 4.1 17.3 1.0
CD1 B:TYR666 4.4 18.3 1.0
CE2 B:TYR631 4.4 16.1 1.0
CZ3 B:TRP659 4.4 17.2 1.0
CE2 B:TYR662 4.4 16.4 1.0
CG2 B:VAL656 4.4 15.6 1.0
OG B:SER630 4.5 28.2 1.0
OH B:TYR547 4.5 28.3 1.0
CE2 B:TYR666 4.6 17.1 1.0
CZ B:TYR662 4.7 16.7 1.0
O B:HOH1022 4.7 30.2 1.0
CD2 B:TYR662 4.8 15.7 1.0
C6 B:2VH801 4.9 17.7 1.0
OH B:TYR662 4.9 17.3 1.0

Fluorine binding site 6 out of 6 in 4pnz

Go back to Fluorine Binding Sites List in 4pnz
Fluorine binding site 6 out of 6 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:20.1
occ:1.00
 F1 B:2VH801 0.0 20.1 1.0
C2 B:2VH801 1.4 21.6 1.0
C1 B:2VH801 2.3 19.6 1.0
C3 B:2VH801 2.4 20.9 1.0
C6 B:2VH801 2.8 17.7 1.0
ND2 B:ASN710 3.2 14.8 1.0
NH2 B:ARG125 3.2 23.0 1.0
OE2 B:GLU205 3.4 19.3 1.0
OD1 B:ASN710 3.4 18.4 1.0
N B:2VH801 3.5 17.8 1.0
O B:HOH1108 3.5 32.7 1.0
OH B:TYR662 3.5 17.3 1.0
CG B:ASN710 3.6 20.6 1.0
C B:2VH801 3.6 21.6 1.0
C4 B:2VH801 3.6 22.4 1.0
C10 B:2VH801 3.7 17.7 1.0
CD2 B:HIS740 3.8 19.2 1.0
O B:HOH1008 3.9 22.6 1.0
NE2 B:HIS740 3.9 18.9 1.0
O B:2VH801 4.0 20.1 1.0
OG B:SER630 4.0 28.2 1.0
C5 B:2VH801 4.1 23.3 1.0
CD B:GLU205 4.5 24.8 1.0
CZ B:ARG125 4.5 37.0 1.0
O B:HOH1619 4.5 48.0 1.0
CZ B:TYR662 4.6 16.7 1.0
F2 B:2VH801 4.7 21.5 1.0
C9 B:2VH801 4.7 17.7 1.0
CB B:ASN710 4.8 13.9 1.0
CG B:HIS740 4.8 17.4 1.0
C7 B:2VH801 4.8 18.7 1.0
CE1 B:HIS740 4.9 18.8 1.0

Reference:

T.Biftu, R.Sinha-Roy, P.Chen, X.Qian, D.Feng, J.T.Kuethe, G.Scapin, Y.D.Gao, Y.Yan, D.Krueger, A.Bak, G.Eiermann, J.He, J.Cox, J.Hicks, K.Lyons, H.He, G.Salituro, S.Tong, S.Patel, G.Doss, A.Petrov, J.Wu, S.S.Xu, C.Sewall, X.Zhang, B.Zhang, N.A.Thornberry, A.E.Weber. Omarigliptin (Mk-3102): A Novel Long-Acting Dpp-4 Inhibitor For Once-Weekly Treatment of Type 2 Diabetes. J.Med.Chem. V. 57 3205 2014.
ISSN: ISSN 0022-2623
PubMed: 24660890
DOI: 10.1021/JM401992E
Page generated: Thu Aug 1 04:56:01 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy