Sodium in PDB 6yq1: Focal Adhesion Kinase Catalytic Domain in Complex with N-Methyl-N-(3- {[2-(2-Oxo-1,2,3,4-Tetrahydro-Quinolin-6-Ylamino)-5-Trifluoromethyl- Pyrimidin-4-Ylamino]-Methyl}-Pyridin-2-Yl)-Methanesulfonamide

Enzymatic activity of Focal Adhesion Kinase Catalytic Domain in Complex with N-Methyl-N-(3- {[2-(2-Oxo-1,2,3,4-Tetrahydro-Quinolin-6-Ylamino)-5-Trifluoromethyl- Pyrimidin-4-Ylamino]-Methyl}-Pyridin-2-Yl)-Methanesulfonamide

All present enzymatic activity of Focal Adhesion Kinase Catalytic Domain in Complex with N-Methyl-N-(3- {[2-(2-Oxo-1,2,3,4-Tetrahydro-Quinolin-6-Ylamino)-5-Trifluoromethyl- Pyrimidin-4-Ylamino]-Methyl}-Pyridin-2-Yl)-Methanesulfonamide:
2.7.10.2;

Protein crystallography data

The structure of Focal Adhesion Kinase Catalytic Domain in Complex with N-Methyl-N-(3- {[2-(2-Oxo-1,2,3,4-Tetrahydro-Quinolin-6-Ylamino)-5-Trifluoromethyl- Pyrimidin-4-Ylamino]-Methyl}-Pyridin-2-Yl)-Methanesulfonamide, PDB code: 6yq1 was solved by D.Musil, T.Heinrich, M.Amaral, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	169.25 / 1.78
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	112.532, 75.749, 173.265, 90, 102.37, 90
*R / R_free (%)*	18.3 / 21.4

Other elements in 6yq1:

The structure of Focal Adhesion Kinase Catalytic Domain in Complex with N-Methyl-N-(3- {[2-(2-Oxo-1,2,3,4-Tetrahydro-Quinolin-6-Ylamino)-5-Trifluoromethyl- Pyrimidin-4-Ylamino]-Methyl}-Pyridin-2-Yl)-Methanesulfonamide also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Focal Adhesion Kinase Catalytic Domain in Complex with N-Methyl-N-(3- {[2-(2-Oxo-1,2,3,4-Tetrahydro-Quinolin-6-Ylamino)-5-Trifluoromethyl- Pyrimidin-4-Ylamino]-Methyl}-Pyridin-2-Yl)-Methanesulfonamide (pdb code 6yq1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Focal Adhesion Kinase Catalytic Domain in Complex with N-Methyl-N-(3- {[2-(2-Oxo-1,2,3,4-Tetrahydro-Quinolin-6-Ylamino)-5-Trifluoromethyl- Pyrimidin-4-Ylamino]-Methyl}-Pyridin-2-Yl)-Methanesulfonamide, PDB code: 6yq1:

Sodium binding site 1 out of 1 in 6yq1

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Sodium Binding Sites List in 6yq1

Sodium binding site 1 out of 1 in the Focal Adhesion Kinase Catalytic Domain in Complex with N-Methyl-N-(3- {[2-(2-Oxo-1,2,3,4-Tetrahydro-Quinolin-6-Ylamino)-5-Trifluoromethyl- Pyrimidin-4-Ylamino]-Methyl}-Pyridin-2-Yl)-Methanesulfonamide

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Focal Adhesion Kinase Catalytic Domain in Complex with N-Methyl-N-(3- {[2-(2-Oxo-1,2,3,4-Tetrahydro-Quinolin-6-Ylamino)-5-Trifluoromethyl- Pyrimidin-4-Ylamino]-Methyl}-Pyridin-2-Yl)-Methanesulfonamide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na702 b:60.2 occ:1.00	OE1	A:GLU416	2.2	61.0	1.0
	OE1	A:GLU492	2.2	49.7	1.0
	O	A:ILE417	2.6	30.9	1.0
	CD	A:GLU492	3.2	50.0	1.0
	CD	A:GLU416	3.4	60.5	1.0
	OE2	A:GLU492	3.5	53.2	1.0
	C	A:ILE417	3.6	31.6	1.0
	CG2	A:ILE490	3.7	30.7	1.0
	CA	A:ILE490	4.0	29.6	1.0
	OE2	A:GLU416	4.1	62.5	1.0
	CA	A:GLN418	4.1	29.6	1.0
	N	A:GLN418	4.2	30.4	1.0
	N	A:THR491	4.3	31.6	1.0
	CB	A:ILE490	4.3	29.9	1.0
	N	A:ILE417	4.4	36.4	1.0
	C	A:ILE490	4.6	30.6	1.0
	CG	A:GLU492	4.6	42.5	1.0
	CG	A:GLU416	4.6	52.4	1.0
	O	A:VAL489	4.6	28.6	1.0
	CA	A:ILE417	4.7	34.1	1.0
	CG1	A:ILE490	4.7	31.2	1.0
	CG	A:GLN418	4.8	38.8	1.0
	N	A:GLU492	4.8	33.6	1.0
	CB	A:GLU416	4.8	45.4	1.0
	N	A:ARG419	4.9	27.2	1.0
	CB	A:GLU492	5.0	36.7	1.0
	C	A:GLN418	5.0	28.0	1.0

Reference:

B.T.Berger, M.Amaral, D.B.Kokh, A.Nunes-Alves, D.Musil, T.Heinrich, M.Schroder, R.Neil, J.Wang, I.Navratilova, J.Bomke, J.M.Elkins, S.Muller, M.Frech, R.C.Wade, S.Knapp. Structure-Kinetic Relationship Reveals the Mechanism of Selectivity of Fak Inhibitors Over PYK2. Cell Chem Biol 2021.
ISSN: ESSN 2451-9456
PubMed: 33497606
DOI: 10.1016/J.CHEMBIOL.2021.01.003

Page generated: Tue Oct 8 15:12:00 2024

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