Fluorine in PDB 7vjl: The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide

Enzymatic activity of The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide

All present enzymatic activity of The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide:
2.7.10.1;

Protein crystallography data

The structure of The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide, PDB code: 7vjl was solved by Z.M.Zhang, Y.J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.91 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.37, 66.785, 184.174, 90, 90, 90
R / Rfree (%) 20.5 / 27.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide (pdb code 7vjl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide, PDB code: 7vjl:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7vjl

Go back to Fluorine Binding Sites List in 7vjl
Fluorine binding site 1 out of 6 in the The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:84.8
occ:1.00
 FAN A:7IF801 0.0 84.8 1.0
CAM A:7IF801 1.3 68.7 1.0
FAP A:7IF801 2.2 69.7 1.0
FAO A:7IF801 2.2 59.0 1.0
CAK A:7IF801 2.3 62.3 1.0
O A:VAL500 2.3 57.1 1.0
OAL A:7IF801 2.5 72.9 1.0
C A:VAL500 2.9 51.6 1.0
N A:VAL500 3.3 47.8 1.0
CA A:VAL500 3.5 47.1 1.0
CG2 A:THR499 3.5 60.9 1.0
CAB A:7IF801 3.6 66.6 1.0
C A:THR499 3.7 58.8 1.0
SG A:CYS552 3.7 76.1 1.0
N A:ALA501 3.7 54.6 1.0
CB A:CYS552 3.9 60.0 1.0
N A:ALA484 3.9 56.7 1.0
O A:ALA484 4.1 55.7 1.0
CG A:ARG483 4.1 58.4 1.0
O A:THR499 4.1 62.8 1.0
CB A:THR499 4.1 60.3 1.0
CA A:ALA501 4.2 54.7 1.0
CA A:ARG483 4.3 58.5 1.0
CAC A:7IF801 4.4 72.0 1.0
NAA A:7IF801 4.4 71.3 1.0
CA A:THR499 4.4 69.4 1.0
CB A:ALA501 4.6 61.3 1.0
C A:ARG483 4.6 56.1 1.0
CB A:ARG483 4.8 53.0 1.0
C A:ALA484 4.9 60.9 1.0
CB A:VAL500 4.9 37.8 1.0
CA A:ALA484 4.9 63.8 1.0
O A:VAL482 5.0 58.4 1.0

Fluorine binding site 2 out of 6 in 7vjl

Go back to Fluorine Binding Sites List in 7vjl
Fluorine binding site 2 out of 6 in the The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:59.0
occ:1.00
 FAO A:7IF801 0.0 59.0 1.0
CAM A:7IF801 1.4 68.7 1.0
FAN A:7IF801 2.2 84.8 1.0
FAP A:7IF801 2.2 69.7 1.0
CAK A:7IF801 2.3 62.3 1.0
SG A:CYS552 2.7 76.1 1.0
CB A:CYS552 3.0 60.0 1.0
CAB A:7IF801 3.2 66.6 1.0
CB A:ALA501 3.3 61.3 1.0
NAA A:7IF801 3.3 71.3 1.0
OAL A:7IF801 3.4 72.9 1.0
O A:VAL500 3.4 57.1 1.0
C A:VAL500 3.5 51.6 1.0
N A:ALA501 3.6 54.6 1.0
CA A:ALA501 3.6 54.7 1.0
NAY A:7IF801 3.6 51.7 1.0
CA A:CYS552 3.7 52.6 1.0
NAS A:7IF801 3.9 47.1 1.0
CD2 A:LEU473 4.0 65.0 1.0
CAT A:7IF801 4.1 47.9 1.0
CA A:VAL500 4.5 47.1 1.0
CAX A:7IF801 4.5 54.6 1.0
CAC A:7IF801 4.5 72.0 1.0
CAF A:7IF801 4.6 69.7 1.0
N A:CYS552 4.7 48.1 1.0
N A:ALA553 4.7 39.0 1.0
C A:CYS552 4.8 52.9 1.0
N A:VAL500 4.9 47.8 1.0
O A:GLU551 5.0 45.2 1.0

Fluorine binding site 3 out of 6 in 7vjl

Go back to Fluorine Binding Sites List in 7vjl
Fluorine binding site 3 out of 6 in the The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:69.7
occ:1.00
 FAP A:7IF801 0.0 69.7 1.0
CAM A:7IF801 1.4 68.7 1.0
FAN A:7IF801 2.2 84.8 1.0
FAO A:7IF801 2.2 59.0 1.0
CAK A:7IF801 2.3 62.3 1.0
CAB A:7IF801 2.7 66.6 1.0
NAA A:7IF801 3.1 71.3 1.0
CG A:ARG483 3.2 58.4 1.0
CD2 A:LEU473 3.3 65.0 1.0
OAL A:7IF801 3.3 72.9 1.0
CAC A:7IF801 3.5 72.0 1.0
CA A:ARG483 3.6 58.5 1.0
CB A:ARG483 3.7 53.0 1.0
SG A:CYS552 3.8 76.1 1.0
O A:VAL500 3.9 57.1 1.0
CD A:ARG483 4.0 70.3 1.0
CAF A:7IF801 4.1 69.7 1.0
NE A:ARG483 4.3 77.2 1.0
N A:ARG483 4.4 64.6 1.0
CAD A:7IF801 4.5 80.2 1.0
NAS A:7IF801 4.5 47.1 1.0
N A:ALA484 4.5 56.7 1.0
CG A:LEU473 4.5 73.4 1.0
C A:VAL500 4.6 51.6 1.0
C A:ARG483 4.6 56.1 1.0
O A:VAL482 4.7 58.4 1.0
CAE A:7IF801 4.7 76.0 1.0
CB A:CYS552 4.8 60.0 1.0
CG2 A:THR499 4.9 60.9 1.0
CD1 A:LEU473 4.9 72.7 1.0
C A:VAL482 4.9 60.6 1.0
CA A:ALA501 4.9 54.7 1.0
CB A:ALA501 5.0 61.3 1.0

Fluorine binding site 4 out of 6 in 7vjl

Go back to Fluorine Binding Sites List in 7vjl
Fluorine binding site 4 out of 6 in the The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:77.4
occ:1.00
 FAN B:7IF801 0.0 77.4 1.0
CAM B:7IF801 1.3 54.9 1.0
FAP B:7IF801 2.2 52.3 1.0
FAO B:7IF801 2.2 40.4 1.0
CAK B:7IF801 2.2 63.1 1.0
OAL B:7IF801 2.6 67.3 1.0
O B:VAL500 3.0 41.6 1.0
CB B:ARG483 3.1 35.7 1.0
CG2 B:THR499 3.3 42.4 1.0
CAB B:7IF801 3.5 79.5 1.0
CA B:ARG483 3.5 27.9 1.0
C B:VAL500 3.5 28.6 1.0
N B:VAL500 3.9 23.8 1.0
SG B:CYS552 3.9 67.8 1.0
N B:ALA484 4.0 33.6 1.0
CG B:ARG483 4.1 44.9 1.0
CA B:VAL500 4.1 21.0 1.0
N B:ALA501 4.1 20.6 1.0
CB B:THR499 4.2 40.5 1.0
CAC B:7IF801 4.2 81.1 1.0
C B:THR499 4.2 33.2 1.0
C B:ARG483 4.2 26.7 1.0
NAA B:7IF801 4.3 74.9 1.0
CB B:CYS552 4.3 26.5 1.0
CD B:ARG483 4.5 51.3 1.0
CA B:ALA501 4.5 21.4 1.0
CD2 B:LEU473 4.7 50.1 1.0
O B:THR499 4.7 36.2 1.0
CA B:THR499 4.7 28.1 1.0
N B:ARG483 4.7 33.7 1.0
O B:ALA484 4.7 21.9 1.0
CB B:ALA501 5.0 21.6 1.0
O B:VAL482 5.0 47.6 1.0

Fluorine binding site 5 out of 6 in 7vjl

Go back to Fluorine Binding Sites List in 7vjl
Fluorine binding site 5 out of 6 in the The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:40.4
occ:1.00
 FAO B:7IF801 0.0 40.4 1.0
CAM B:7IF801 1.4 54.9 1.0
FAN B:7IF801 2.2 77.4 1.0
FAP B:7IF801 2.2 52.3 1.0
CAK B:7IF801 2.3 63.1 1.0
CAB B:7IF801 2.6 79.5 1.0
NAA B:7IF801 2.8 74.9 1.0
CD2 B:LEU473 3.2 50.1 1.0
SG B:CYS552 3.4 67.8 1.0
CG B:LEU473 3.5 43.9 1.0
CB B:ARG483 3.5 35.7 1.0
OAL B:7IF801 3.6 67.3 1.0
CAC B:7IF801 3.7 81.1 1.0
CD1 B:LEU473 3.8 37.5 1.0
NAS B:7IF801 3.8 54.3 1.0
CAF B:7IF801 3.9 62.0 1.0
CA B:ARG483 4.0 27.9 1.0
O B:VAL500 4.4 41.6 1.0
CAT B:7IF801 4.5 55.0 1.0
CB B:ALA501 4.5 21.6 1.0
CB B:CYS552 4.5 26.5 1.0
CAQ B:7IF801 4.6 59.6 1.0
CAD B:7IF801 4.6 73.4 1.0
NAJ B:7IF801 4.6 59.8 1.0
CA B:ALA501 4.6 21.4 1.0
CAE B:7IF801 4.7 57.2 1.0
NAY B:7IF801 4.7 53.2 1.0
N B:ARG483 4.7 33.7 1.0
CG B:ARG483 4.8 44.9 1.0
C B:VAL500 4.8 28.6 1.0
N B:ALA501 4.9 20.6 1.0
O B:VAL482 4.9 47.6 1.0
CD B:ARG483 4.9 51.3 1.0
CB B:LEU473 4.9 38.6 1.0
NE B:ARG483 5.0 52.8 1.0

Fluorine binding site 6 out of 6 in 7vjl

Go back to Fluorine Binding Sites List in 7vjl
Fluorine binding site 6 out of 6 in the The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Crystal Structure of FGFR4 Kinase Domain in Complex with N-(5- Cyano-4-((2-Methoxyethyl)Amino)Pyridin-2-Yl)-7-(2,2,2- Trifluoroacetyl)-3,4-Dihydro-1,8-Naphthyridine-1(2H)-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:52.3
occ:1.00
 FAP B:7IF801 0.0 52.3 1.0
CAM B:7IF801 1.4 54.9 1.0
FAN B:7IF801 2.2 77.4 1.0
FAO B:7IF801 2.2 40.4 1.0
CAK B:7IF801 2.4 63.1 1.0
SG B:CYS552 2.7 67.8 1.0
CB B:CYS552 2.8 26.5 1.0
N B:ALA501 3.2 20.6 1.0
OAL B:7IF801 3.2 67.3 1.0
C B:VAL500 3.2 28.6 1.0
CB B:ALA501 3.4 21.6 1.0
O B:VAL500 3.4 41.6 1.0
CA B:ALA501 3.5 21.4 1.0
CA B:CYS552 3.5 32.7 1.0
CAB B:7IF801 3.5 79.5 1.0
NAA B:7IF801 3.8 74.9 1.0
CA B:VAL500 3.9 21.0 1.0
NAY B:7IF801 4.2 53.2 1.0
N B:CYS552 4.2 18.5 1.0
N B:VAL500 4.3 23.8 1.0
NAS B:7IF801 4.4 54.3 1.0
CAT B:7IF801 4.6 55.0 1.0
O B:GLU551 4.6 20.0 1.0
C B:CYS552 4.7 24.2 1.0
O B:THR499 4.7 36.2 1.0
C B:THR499 4.7 33.2 1.0
C B:GLU551 4.7 20.1 1.0
CAC B:7IF801 4.7 81.1 1.0
N B:ALA553 4.8 21.4 1.0
CB B:ARG483 4.8 35.7 1.0
CA B:ARG483 4.9 27.9 1.0
CD2 B:LEU473 4.9 50.1 1.0
CAX B:7IF801 4.9 50.7 1.0
C B:ALA501 5.0 31.7 1.0

Reference:

Z.Zhang, Y.Wang, X.Chen, X.Song, Z.Tu, Y.Chen, Z.Zhang, K.Ding. Characterization of An Aromatic Trifluoromethyl Ketone As A New Warhead For Covalently Reversible Kinase Inhibitor Design. Bioorg.Med.Chem. V. 50 16457 2021.
ISSN: ESSN 1464-3391
PubMed: 34670167
DOI: 10.1016/J.BMC.2021.116457
Page generated: Wed Apr 5 01:35:17 2023

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