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Fluorine in PDB 3kwf: Human Dpp-IV with Carmegliptin (S)-1-((2S,3S,11BS)-2-Amino- 9,10-Dimethoxy-1,3,4,6,7,11B-Hexahydro-2H-Pyrido[2,1- A]Isoquinolin-3-Yl)-4-Fluoromethyl-Pyrrolidin-2-One

Enzymatic activity of Human Dpp-IV with Carmegliptin (S)-1-((2S,3S,11BS)-2-Amino- 9,10-Dimethoxy-1,3,4,6,7,11B-Hexahydro-2H-Pyrido[2,1- A]Isoquinolin-3-Yl)-4-Fluoromethyl-Pyrrolidin-2-One

All present enzymatic activity of Human Dpp-IV with Carmegliptin (S)-1-((2S,3S,11BS)-2-Amino- 9,10-Dimethoxy-1,3,4,6,7,11B-Hexahydro-2H-Pyrido[2,1- A]Isoquinolin-3-Yl)-4-Fluoromethyl-Pyrrolidin-2-One:
3.4.14.5;

Protein crystallography data

The structure of Human Dpp-IV with Carmegliptin (S)-1-((2S,3S,11BS)-2-Amino- 9,10-Dimethoxy-1,3,4,6,7,11B-Hexahydro-2H-Pyrido[2,1- A]Isoquinolin-3-Yl)-4-Fluoromethyl-Pyrrolidin-2-One, PDB code: 3kwf was solved by M.Hennig, M.Stihle, R.Thoma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.626, 69.541, 423.039, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Dpp-IV with Carmegliptin (S)-1-((2S,3S,11BS)-2-Amino- 9,10-Dimethoxy-1,3,4,6,7,11B-Hexahydro-2H-Pyrido[2,1- A]Isoquinolin-3-Yl)-4-Fluoromethyl-Pyrrolidin-2-One (pdb code 3kwf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Human Dpp-IV with Carmegliptin (S)-1-((2S,3S,11BS)-2-Amino- 9,10-Dimethoxy-1,3,4,6,7,11B-Hexahydro-2H-Pyrido[2,1- A]Isoquinolin-3-Yl)-4-Fluoromethyl-Pyrrolidin-2-One, PDB code: 3kwf:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3kwf

Go back to Fluorine Binding Sites List in 3kwf
Fluorine binding site 1 out of 2 in the Human Dpp-IV with Carmegliptin (S)-1-((2S,3S,11BS)-2-Amino- 9,10-Dimethoxy-1,3,4,6,7,11B-Hexahydro-2H-Pyrido[2,1- A]Isoquinolin-3-Yl)-4-Fluoromethyl-Pyrrolidin-2-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Dpp-IV with Carmegliptin (S)-1-((2S,3S,11BS)-2-Amino- 9,10-Dimethoxy-1,3,4,6,7,11B-Hexahydro-2H-Pyrido[2,1- A]Isoquinolin-3-Yl)-4-Fluoromethyl-Pyrrolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:30.9
occ:1.00
F24 A:B1Q1 0.0 30.9 1.0
C25 A:B1Q1 1.4 27.7 1.0
C18 A:B1Q1 2.3 25.6 1.0
C13 A:B1Q1 3.1 25.5 1.0
CG2 A:VAL656 3.6 27.4 1.0
CH2 A:TRP659 3.6 28.6 1.0
C16 A:B1Q1 3.6 25.6 1.0
CD2 A:TYR631 3.7 29.9 1.0
CZ3 A:TRP659 3.8 27.9 1.0
CE1 A:TYR666 4.0 28.5 1.0
OH A:TYR666 4.1 30.5 1.0
CZ A:TYR666 4.1 29.7 1.0
CB A:TYR631 4.1 29.0 1.0
CA A:TYR631 4.3 29.4 1.0
CE2 A:TYR662 4.3 24.2 1.0
N A:TYR631 4.3 30.3 1.0
CG A:TYR631 4.3 28.5 1.0
N1 A:B1Q1 4.4 26.2 1.0
CD2 A:TYR662 4.4 25.1 1.0
CB A:VAL656 4.6 27.4 1.0
CZ A:TYR662 4.6 24.9 1.0
CE2 A:TYR631 4.6 28.6 1.0
C5 A:B1Q1 4.7 26.0 1.0
CD1 A:TYR666 4.7 28.6 1.0
CZ2 A:TRP659 4.7 28.2 1.0
CG A:TYR662 4.9 25.9 1.0
CE2 A:TYR666 4.9 28.4 1.0
C A:SER630 5.0 31.3 1.0
CE1 A:TYR662 5.0 24.0 1.0

Fluorine binding site 2 out of 2 in 3kwf

Go back to Fluorine Binding Sites List in 3kwf
Fluorine binding site 2 out of 2 in the Human Dpp-IV with Carmegliptin (S)-1-((2S,3S,11BS)-2-Amino- 9,10-Dimethoxy-1,3,4,6,7,11B-Hexahydro-2H-Pyrido[2,1- A]Isoquinolin-3-Yl)-4-Fluoromethyl-Pyrrolidin-2-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Dpp-IV with Carmegliptin (S)-1-((2S,3S,11BS)-2-Amino- 9,10-Dimethoxy-1,3,4,6,7,11B-Hexahydro-2H-Pyrido[2,1- A]Isoquinolin-3-Yl)-4-Fluoromethyl-Pyrrolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:30.8
occ:1.00
F24 B:B1Q1 0.0 30.8 1.0
C25 B:B1Q1 1.4 30.8 1.0
C18 B:B1Q1 2.4 29.2 1.0
C13 B:B1Q1 3.0 27.9 1.0
CD2 B:TYR631 3.2 31.7 1.0
CH2 B:TRP659 3.3 29.7 1.0
CZ3 B:TRP659 3.7 29.6 1.0
C16 B:B1Q1 3.7 28.3 1.0
CB B:TYR631 3.7 31.7 1.0
CG2 B:VAL656 3.8 29.0 1.0
OH B:TYR666 3.8 27.3 1.0
CE1 B:TYR666 3.9 27.6 1.0
CG B:TYR631 3.9 31.9 1.0
CZ B:TYR666 4.0 27.8 1.0
CA B:TYR631 4.1 31.2 1.0
CE2 B:TYR631 4.1 32.6 1.0
N B:TYR631 4.3 31.3 1.0
N1 B:B1Q1 4.3 26.8 1.0
CZ2 B:TRP659 4.4 29.4 1.0
CE2 B:TYR662 4.6 27.3 1.0
C5 B:B1Q1 4.7 27.1 1.0
CD1 B:TYR666 4.7 26.2 1.0
CB B:VAL656 4.7 29.1 1.0
CD2 B:TYR662 4.7 27.9 1.0
CZ B:TYR662 4.9 27.4 1.0
CE2 B:TYR666 4.9 26.6 1.0
OG B:SER630 4.9 32.6 1.0
O B:HOH871 4.9 30.0 1.0

Reference:

P.Mattei, M.Boehringer, P.Di Giorgio, H.Fischer, M.Hennig, J.Huwyler, B.Kocer, B.Kuhn, B.M.Loeffler, A.Macdonald, R.Narquizian, E.Rauber, E.Sebokova, U.Sprecher. Discovery of Carmegliptin: A Potent and Long-Acting Dipeptidyl Peptidase IV Inhibitor For the Treatment of Type 2 Diabetes. Bioorg.Med.Chem.Lett. V. 20 1109 2010.
ISSN: ISSN 0960-894X
PubMed: 20031405
DOI: 10.1016/J.BMCL.2009.12.024
Page generated: Mon Jul 14 17:38:40 2025

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