Chlorine in PDB 6nvg: FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide

Enzymatic activity of FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide

All present enzymatic activity of FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide:
2.7.10.1;

Protein crystallography data

The structure of FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide, PDB code: 6nvg was solved by X.Lin, J.B.Smaill, C.J.Squire, Y.Yosaatmadja, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.18 / 1.99
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 63.731, 63.731, 182.849, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide (pdb code 6nvg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide, PDB code: 6nvg:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6nvg

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Chlorine binding site 1 out of 4 in the FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:45.3
occ:1.00
 CL1 A:XL8804 0.0 45.3 1.0
C2 A:XL8804 1.7 41.2 1.0
C1 A:XL8804 2.7 37.5 1.0
C3 A:XL8804 2.7 42.9 1.0
O1 A:XL8804 2.9 40.1 1.0
C9 A:XL8804 3.0 42.7 1.0
O3 A:XL8804 3.2 39.9 1.0
CB A:ALA620 3.3 39.2 1.0
CD1 A:LEU610 3.7 35.6 1.0
OD1 A:ASP621 3.8 49.3 1.0
C10 A:XL8804 3.9 38.4 1.0
CG1 A:ILE534 3.9 29.8 1.0
CG2 A:ILE534 3.9 33.6 1.0
C4 A:XL8804 4.0 44.1 1.0
CA A:ALA620 4.0 34.0 1.0
C6 A:XL8804 4.0 38.3 1.0
C7 A:XL8804 4.1 41.9 1.0
CB A:ILE534 4.2 33.9 1.0
N A:ASP621 4.2 33.8 1.0
C13 A:XL8804 4.3 40.1 1.0
C5 A:XL8804 4.5 42.6 1.0
C11 A:XL8804 4.6 43.8 1.0
CD1 A:ILE534 4.6 29.3 1.0
CG A:LEU610 4.6 35.3 1.0
C A:ALA620 4.6 32.1 1.0
CG A:ASP621 4.7 48.5 1.0

Chlorine binding site 2 out of 4 in 6nvg

Go back to Chlorine Binding Sites List in 6nvg
Chlorine binding site 2 out of 4 in the FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:49.5
occ:1.00
 CL2 A:XL8804 0.0 49.5 1.0
C4 A:XL8804 1.7 44.1 1.0
C3 A:XL8804 2.7 42.9 1.0
C5 A:XL8804 2.7 42.6 1.0
O2 A:XL8804 2.9 36.8 1.0
C9 A:XL8804 3.0 42.7 1.0
CG1 A:VAL481 3.6 42.0 1.0
CB A:LYS503 3.6 40.6 1.0
O3 A:XL8804 3.7 39.9 1.0
CG2 A:VAL550 3.8 34.9 1.0
CG2 A:VAL481 3.8 44.9 1.0
N A:LYS503 3.8 39.9 1.0
C2 A:XL8804 4.0 41.2 1.0
C6 A:XL8804 4.0 38.3 1.0
CA A:LYS503 4.1 40.3 1.0
C A:VAL502 4.2 42.6 1.0
CB A:ALA501 4.3 37.9 1.0
CE A:LYS503 4.3 47.6 1.0
CB A:VAL481 4.3 41.6 1.0
C8 A:XL8804 4.4 41.2 1.0
CG A:LYS503 4.5 44.8 1.0
C1 A:XL8804 4.5 37.5 1.0
C A:ALA501 4.6 39.6 1.0
N A:VAL502 4.6 34.7 1.0
O A:ALA501 4.6 39.9 1.0
O A:VAL502 4.7 41.3 1.0
CA A:VAL502 4.8 38.0 1.0
CG1 A:VAL550 4.8 35.3 1.0
O A:VAL548 4.9 39.3 1.0
CD A:LYS503 4.9 44.7 1.0
C10 A:XL8804 4.9 38.4 1.0
CB A:VAL550 4.9 38.8 1.0

Chlorine binding site 3 out of 4 in 6nvg

Go back to Chlorine Binding Sites List in 6nvg
Chlorine binding site 3 out of 4 in the FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:51.1
occ:1.00
 CL3 A:XL8804 0.0 51.1 1.0
C19 A:XL8804 1.7 49.5 1.0
C18 A:XL8804 2.7 55.6 1.0
C14 A:XL8804 2.7 51.8 1.0
N3 A:XL8804 3.0 51.0 1.0
N1 A:XL8804 3.2 43.5 1.0
C12 A:XL8804 3.3 40.4 1.0
CA A:GLY556 3.7 41.5 1.0
CD2 A:LEU610 3.7 38.1 1.0
C A:GLY556 4.0 41.4 1.0
C17 A:XL8804 4.0 66.5 1.0
N A:ASN557 4.0 33.7 1.0
C15 A:XL8804 4.0 52.6 1.0
CD1 A:LEU610 4.1 35.6 1.0
C11 A:XL8804 4.1 43.8 1.0
N2 A:XL8804 4.3 47.4 1.0
O A:HOH966 4.4 47.5 1.0
CG A:LEU610 4.4 35.3 1.0
C16 A:XL8804 4.5 53.3 1.0
O A:GLY556 4.6 42.6 1.0
N A:GLY556 4.7 41.4 1.0
CB A:ASN557 4.8 36.9 1.0
CA A:ASN557 4.9 33.0 1.0
C10 A:XL8804 5.0 38.4 1.0

Chlorine binding site 4 out of 4 in 6nvg

Go back to Chlorine Binding Sites List in 6nvg
Chlorine binding site 4 out of 4 in the FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of FGFR4 Complex with N-(3,5-Dichloro-2-((5-((2,6-Dichloro-3,5- Dimethoxybenzyl)Oxy)Pyrimidin-2-Yl)Amino)Phenyl)Acrylamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:60.0
occ:1.00
 CL4 A:XL8804 0.0 60.0 1.0
C17 A:XL8804 1.7 66.5 1.0
C18 A:XL8804 2.7 55.6 1.0
C16 A:XL8804 2.7 53.3 1.0
C19 A:XL8804 4.0 49.5 1.0
C15 A:XL8804 4.0 52.6 1.0
C14 A:XL8804 4.5 51.8 1.0
O A:HOH976 4.6 62.0 1.0
O A:HOH966 4.7 47.5 1.0
CD2 A:LEU473 4.8 62.6 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: Sat Dec 12 13:24:56 2020

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