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Chlorine in PDB 6nvl: FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide

Enzymatic activity of FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide

All present enzymatic activity of FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide:
2.7.10.1;

Protein crystallography data

The structure of FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide, PDB code: 6nvl was solved by X.Lin, J.B.Smaill, C.J.Squire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.06 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 93.331, 83.701, 102.604, 90.00, 113.60, 90.00
R / Rfree (%) 21.3 / 26.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide (pdb code 6nvl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide, PDB code: 6nvl:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6nvl

Go back to Chlorine Binding Sites List in 6nvl
Chlorine binding site 1 out of 8 in the FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl802

b:45.1
occ:1.00
 CL1 A:XL6802 0.0 45.1 1.0
C2 A:XL6802 1.7 42.6 1.0
C1 A:XL6802 2.7 43.4 1.0
C3 A:XL6802 2.7 40.4 1.0
O1 A:XL6802 2.9 44.2 1.0
C9 A:XL6802 3.0 38.6 1.0
CB A:ALA640 3.1 33.0 1.0
O3 A:XL6802 3.4 36.9 1.0
CD1 A:LEU630 3.5 26.4 1.0
OD1 A:ASP641 3.8 47.8 1.0
CA A:ALA640 3.8 33.8 1.0
CG1 A:ILE545 3.9 25.0 1.0
C4 A:XL6802 4.0 40.6 1.0
C6 A:XL6802 4.0 41.3 1.0
C10 A:XL6802 4.1 36.6 1.0
CG2 A:ILE545 4.1 24.6 1.0
N A:ASP641 4.2 39.0 1.0
C7 A:XL6802 4.2 43.4 1.0
CB A:ILE545 4.3 24.6 1.0
CG A:LEU630 4.4 26.1 1.0
C5 A:XL6802 4.5 40.0 1.0
C A:ALA640 4.5 35.4 1.0
C11 A:XL6802 4.6 36.6 1.0
CD1 A:ILE545 4.6 25.5 1.0
C13 A:XL6802 4.8 35.8 1.0
CG A:ASP641 4.9 45.7 1.0

Chlorine binding site 2 out of 8 in 6nvl

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Chlorine binding site 2 out of 8 in the FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl802

b:45.7
occ:1.00
 CL2 A:XL6802 0.0 45.7 1.0
C4 A:XL6802 1.7 40.6 1.0
C5 A:XL6802 2.7 40.0 1.0
C3 A:XL6802 2.7 40.4 1.0
O2 A:XL6802 2.9 38.4 1.0
C9 A:XL6802 3.1 38.6 1.0
CG2 A:VAL561 3.6 26.7 1.0
CB A:LYS514 3.7 34.3 1.0
O3 A:XL6802 3.7 36.9 1.0
N A:LYS514 3.8 31.6 1.0
CG1 A:VAL492 3.9 40.1 1.0
CG2 A:VAL492 3.9 39.4 1.0
C A:VAL513 4.0 30.3 1.0
C6 A:XL6802 4.0 41.3 1.0
C2 A:XL6802 4.0 42.6 1.0
CA A:LYS514 4.1 33.5 1.0
CB A:ALA512 4.2 27.1 1.0
O A:VAL513 4.2 29.8 1.0
C8 A:XL6802 4.2 37.1 1.0
N A:VAL513 4.4 28.4 1.0
CG A:LYS514 4.4 35.0 1.0
C A:ALA512 4.5 27.4 1.0
CB A:VAL492 4.5 39.8 1.0
C1 A:XL6802 4.5 43.4 1.0
CA A:VAL513 4.6 29.6 1.0
CD A:LYS514 4.6 37.0 1.0
CG1 A:VAL561 4.7 27.0 1.0
O A:ALA512 4.8 27.6 1.0
CB A:VAL561 4.8 27.2 1.0
O A:VAL559 4.8 28.5 1.0
C10 A:XL6802 4.8 36.6 1.0
CA A:ALA512 5.0 27.5 1.0

Chlorine binding site 3 out of 8 in 6nvl

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Chlorine binding site 3 out of 8 in the FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl802

b:56.5
occ:1.00
 CL1 B:XL6802 0.0 56.5 1.0
C2 B:XL6802 1.7 52.2 1.0
C3 B:XL6802 2.7 50.6 1.0
C1 B:XL6802 2.7 52.0 1.0
O1 B:XL6802 2.9 50.7 1.0
C9 B:XL6802 3.0 48.0 1.0
CB B:ALA640 3.1 35.8 1.0
O3 B:XL6802 3.3 46.5 1.0
CD1 B:LEU630 3.6 29.4 1.0
CA B:ALA640 3.7 35.7 1.0
C10 B:XL6802 3.9 43.7 1.0
C4 B:XL6802 4.0 52.9 1.0
C6 B:XL6802 4.0 53.0 1.0
CG1 B:ILE545 4.0 27.3 1.0
N B:ASP641 4.0 39.0 1.0
C7 B:XL6802 4.1 50.2 1.0
CG2 B:ILE545 4.2 27.2 1.0
OD2 B:ASP641 4.2 50.5 1.0
OD1 B:ASP641 4.3 46.1 1.0
CG B:ASP641 4.3 45.7 1.0
CB B:ILE545 4.3 27.3 1.0
C B:ALA640 4.4 37.6 1.0
C11 B:XL6802 4.5 42.1 1.0
CG B:LEU630 4.5 29.7 1.0
C5 B:XL6802 4.5 53.2 1.0
C13 B:XL6802 4.5 42.6 1.0
CD1 B:ILE545 4.8 27.0 1.0

Chlorine binding site 4 out of 8 in 6nvl

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Chlorine binding site 4 out of 8 in the FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl802

b:57.6
occ:1.00
 CL2 B:XL6802 0.0 57.6 1.0
C4 B:XL6802 1.7 52.9 1.0
C3 B:XL6802 2.7 50.6 1.0
C5 B:XL6802 2.7 53.2 1.0
O2 B:XL6802 2.9 52.2 1.0
C9 B:XL6802 3.0 48.0 1.0
N B:LYS514 3.5 30.5 1.0
CB B:LYS514 3.5 33.5 1.0
CG2 B:VAL492 3.7 36.4 1.0
O3 B:XL6802 3.7 46.5 1.0
C B:VAL513 3.9 29.8 1.0
CA B:LYS514 3.9 32.0 1.0
CG2 B:VAL561 4.0 28.9 1.0
CG1 B:VAL492 4.0 37.4 1.0
C2 B:XL6802 4.0 52.2 1.0
C6 B:XL6802 4.0 53.0 1.0
C8 B:XL6802 4.3 52.1 1.0
O B:VAL513 4.3 29.0 1.0
N B:VAL513 4.3 28.3 1.0
CB B:ALA512 4.3 27.6 1.0
CE B:LYS514 4.3 39.7 1.0
C B:ALA512 4.4 27.5 1.0
CB B:VAL492 4.4 36.2 1.0
O B:ALA512 4.5 27.9 1.0
CA B:VAL513 4.5 29.2 1.0
C1 B:XL6802 4.5 52.0 1.0
O B:VAL559 4.6 26.6 1.0
CG B:LYS514 4.6 34.7 1.0
CA B:VAL492 4.9 36.9 1.0
CG1 B:VAL561 4.9 28.5 1.0
CD B:LYS514 4.9 36.6 1.0
C10 B:XL6802 4.9 43.7 1.0
CA B:ALA512 5.0 27.4 1.0

Chlorine binding site 5 out of 8 in 6nvl

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Chlorine binding site 5 out of 8 in the FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl801

b:54.4
occ:1.00
 CL1 C:XL6801 0.0 54.4 1.0
C2 C:XL6801 1.7 51.0 1.0
C1 C:XL6801 2.7 50.1 1.0
C3 C:XL6801 2.7 50.6 1.0
O1 C:XL6801 2.9 49.1 1.0
C9 C:XL6801 3.1 50.5 1.0
CB C:LYS514 3.6 49.9 1.0
CG2 C:VAL492 3.7 50.7 1.0
CG2 C:VAL561 3.7 31.3 1.0
O3 C:XL6801 3.7 50.4 1.0
CG1 C:VAL492 3.8 49.9 1.0
N C:LYS514 3.8 47.6 1.0
C6 C:XL6801 4.0 48.7 1.0
C4 C:XL6801 4.0 49.7 1.0
CB C:ALA512 4.1 38.9 1.0
C C:VAL513 4.1 45.4 1.0
C7 C:XL6801 4.1 48.5 1.0
CA C:LYS514 4.1 48.1 1.0
CB C:VAL492 4.3 50.7 1.0
C C:ALA512 4.3 39.4 1.0
O C:ALA512 4.4 39.6 1.0
N C:VAL513 4.4 40.9 1.0
CG C:LYS514 4.5 52.8 1.0
C5 C:XL6801 4.5 48.0 1.0
CD C:LYS514 4.5 54.5 1.0
O C:VAL513 4.5 47.0 1.0
CG1 C:VAL561 4.6 30.3 1.0
CA C:VAL513 4.7 43.2 1.0
CB C:VAL561 4.8 31.3 1.0
O C:VAL559 4.8 35.7 1.0
CA C:ALA512 4.9 39.1 1.0
CA C:VAL492 4.9 50.7 1.0
C10 C:XL6801 4.9 51.4 1.0

Chlorine binding site 6 out of 8 in 6nvl

Go back to Chlorine Binding Sites List in 6nvl
Chlorine binding site 6 out of 8 in the FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl801

b:52.0
occ:1.00
 CL2 C:XL6801 0.0 52.0 1.0
C4 C:XL6801 1.7 49.7 1.0
C5 C:XL6801 2.7 48.0 1.0
C3 C:XL6801 2.7 50.6 1.0
O2 C:XL6801 2.9 47.4 1.0
C9 C:XL6801 3.1 50.5 1.0
CB C:ALA640 3.3 30.1 1.0
O3 C:XL6801 3.5 50.4 1.0
N C:ASP641 3.9 35.1 1.0
CD1 C:LEU630 3.9 29.4 1.0
CA C:ALA640 3.9 30.4 1.0
C6 C:XL6801 4.0 48.7 1.0
CG1 C:ILE545 4.0 29.1 1.0
C2 C:XL6801 4.0 51.0 1.0
C10 C:XL6801 4.0 51.4 1.0
C8 C:XL6801 4.1 47.2 1.0
CG2 C:ILE545 4.2 28.4 1.0
CB C:ILE545 4.3 28.9 1.0
C C:ALA640 4.4 32.5 1.0
C1 C:XL6801 4.5 50.1 1.0
C13 C:XL6801 4.6 52.4 1.0
C11 C:XL6801 4.7 50.6 1.0
CG C:LEU630 4.8 28.8 1.0
CD1 C:ILE545 4.8 28.8 1.0
CA C:ASP641 4.9 37.1 1.0

Chlorine binding site 7 out of 8 in 6nvl

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Chlorine binding site 7 out of 8 in the FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl804

b:74.8
occ:1.00
 CL1 D:XL6804 0.0 74.8 1.0
C2 D:XL6804 1.7 72.6 1.0
C1 D:XL6804 2.7 71.6 1.0
C3 D:XL6804 2.7 71.7 1.0
O1 D:XL6804 2.8 70.7 1.0
C9 D:XL6804 3.0 69.2 1.0
O3 D:XL6804 3.1 68.7 1.0
CB D:ALA640 3.3 46.6 1.0
CD1 D:LEU630 3.8 39.3 1.0
CG1 D:ILE545 3.8 51.5 1.0
CG2 D:ILE545 3.8 49.5 1.0
C10 D:XL6804 3.9 65.8 1.0
CA D:ALA640 3.9 46.0 1.0
C6 D:XL6804 4.0 73.5 1.0
C4 D:XL6804 4.0 75.4 1.0
CB D:ILE545 4.1 50.0 1.0
OD1 D:ASP641 4.1 66.9 1.0
C7 D:XL6804 4.2 74.4 1.0
N D:ASP641 4.3 50.1 1.0
C11 D:XL6804 4.5 63.5 1.0
C5 D:XL6804 4.5 76.4 1.0
CD1 D:ILE545 4.6 51.9 1.0
C D:ALA640 4.6 47.4 1.0
C13 D:XL6804 4.7 66.4 1.0
CG D:LEU630 4.8 39.9 1.0

Chlorine binding site 8 out of 8 in 6nvl

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Chlorine binding site 8 out of 8 in the FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of FGFR1 Complex with N-(2-((5-((2,6-Dichloro-3,5-Dimethoxybenzyl)Oxy) Pyrimidin-2-Yl)Amino)-3-Methylphenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl804

b:79.8
occ:1.00
 CL2 D:XL6804 0.0 79.8 1.0
C4 D:XL6804 1.7 75.4 1.0
C5 D:XL6804 2.7 76.4 1.0
C3 D:XL6804 2.7 71.7 1.0
O2 D:XL6804 2.9 78.0 1.0
C9 D:XL6804 3.1 69.2 1.0
CB D:LYS514 3.4 64.9 1.0
N D:LYS514 3.6 60.6 1.0
C8 D:XL6804 3.6 77.6 1.0
CG2 D:VAL561 3.6 52.1 1.0
CA D:LYS514 3.9 64.5 1.0
O3 D:XL6804 3.9 68.7 1.0
CG2 D:VAL492 4.0 62.2 1.0
C2 D:XL6804 4.0 72.6 1.0
C6 D:XL6804 4.0 73.5 1.0
C D:VAL513 4.1 57.2 1.0
CG1 D:VAL492 4.4 62.6 1.0
O D:VAL513 4.5 59.0 1.0
C1 D:XL6804 4.5 71.6 1.0
O D:VAL559 4.6 59.0 1.0
N D:VAL513 4.7 52.2 1.0
CB D:VAL492 4.8 62.2 1.0
CA D:VAL513 4.8 54.3 1.0
C D:ALA512 4.8 50.9 1.0
CB D:ALA512 4.9 53.7 1.0
CG1 D:VAL561 4.9 53.4 1.0
O D:ALA512 4.9 49.4 1.0
CB D:VAL561 4.9 53.7 1.0
C10 D:XL6804 5.0 65.8 1.0

Reference:

X.Lin, Y.Yosaatmadja, M.Kalyukina, M.J.Middleditch, Z.Zhang, X.Lu, K.Ding, A.V.Patterson, J.B.Smaill, C.J.Squire. Rotational Freedom, Steric Hindrance, and Protein Dynamics Explain BLU554 Selectivity For the Hinge Cysteine of FGFR4. Acs Med.Chem.Lett. V. 10 1180 2019.
ISSN: ISSN 1948-5875
PubMed: 31413803
DOI: 10.1021/ACSMEDCHEMLETT.9B00196
Page generated: Mon Jul 29 12:16:31 2024

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