Sodium in PDB 8u2d: Bruton'S Tyrosine Kinase in Complex with N-[(2R)-1-[(3R)-3- (Methylcarbamoyl)-1H,2H,3H,4H,9H-Pyrido[3,4-B]Indol-2-Yl]-3-(3- Methylphenyl)-1-Oxopropan-2-Yl]-1H-Indazole-5-Carboxamide

Enzymatic activity of Bruton'S Tyrosine Kinase in Complex with N-[(2R)-1-[(3R)-3- (Methylcarbamoyl)-1H,2H,3H,4H,9H-Pyrido[3,4-B]Indol-2-Yl]-3-(3- Methylphenyl)-1-Oxopropan-2-Yl]-1H-Indazole-5-Carboxamide

All present enzymatic activity of Bruton'S Tyrosine Kinase in Complex with N-[(2R)-1-[(3R)-3- (Methylcarbamoyl)-1H,2H,3H,4H,9H-Pyrido[3,4-B]Indol-2-Yl]-3-(3- Methylphenyl)-1-Oxopropan-2-Yl]-1H-Indazole-5-Carboxamide:
2.7.10.2;

Protein crystallography data

The structure of Bruton'S Tyrosine Kinase in Complex with N-[(2R)-1-[(3R)-3- (Methylcarbamoyl)-1H,2H,3H,4H,9H-Pyrido[3,4-B]Indol-2-Yl]-3-(3- Methylphenyl)-1-Oxopropan-2-Yl]-1H-Indazole-5-Carboxamide, PDB code: 8u2d was solved by S.Gajewski, M.C.Clifton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	44.32 / 1.95
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	38.39, 79.34, 106.88, 90, 90, 90
*R / R_free (%)*	19.1 / 23.8

Other elements in 8u2d:

The structure of Bruton'S Tyrosine Kinase in Complex with N-[(2R)-1-[(3R)-3- (Methylcarbamoyl)-1H,2H,3H,4H,9H-Pyrido[3,4-B]Indol-2-Yl]-3-(3- Methylphenyl)-1-Oxopropan-2-Yl]-1H-Indazole-5-Carboxamide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Bruton'S Tyrosine Kinase in Complex with N-[(2R)-1-[(3R)-3- (Methylcarbamoyl)-1H,2H,3H,4H,9H-Pyrido[3,4-B]Indol-2-Yl]-3-(3- Methylphenyl)-1-Oxopropan-2-Yl]-1H-Indazole-5-Carboxamide (pdb code 8u2d). 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 Bruton'S Tyrosine Kinase in Complex with N-[(2R)-1-[(3R)-3- (Methylcarbamoyl)-1H,2H,3H,4H,9H-Pyrido[3,4-B]Indol-2-Yl]-3-(3- Methylphenyl)-1-Oxopropan-2-Yl]-1H-Indazole-5-Carboxamide, PDB code: 8u2d:

Sodium binding site 1 out of 1 in 8u2d

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Sodium Binding Sites List in 8u2d

Sodium binding site 1 out of 1 in the Bruton'S Tyrosine Kinase in Complex with N-[(2R)-1-[(3R)-3- (Methylcarbamoyl)-1H,2H,3H,4H,9H-Pyrido[3,4-B]Indol-2-Yl]-3-(3- Methylphenyl)-1-Oxopropan-2-Yl]-1H-Indazole-5-Carboxamide

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bruton'S Tyrosine Kinase in Complex with N-[(2R)-1-[(3R)-3- (Methylcarbamoyl)-1H,2H,3H,4H,9H-Pyrido[3,4-B]Indol-2-Yl]-3-(3- Methylphenyl)-1-Oxopropan-2-Yl]-1H-Indazole-5-Carboxamide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na702 b:31.8 occ:1.00	O1	A:SO4705	2.3	19.7	1.0
	S	A:SO4705	3.4	10.9	1.0
	N	A:ARG600	3.5	33.7	1.0
	CB	A:ARG600	3.5	31.5	1.0
	O3	A:SO4705	3.8	31.7	1.0
	O	A:HOH912	3.8	31.5	1.0
	O2	A:SO4705	3.8	48.5	1.0
	CE2	A:PHE601	3.9	34.9	1.0
	N	A:GLU599	3.9	26.8	1.0
	CD2	A:PHE601	4.0	38.9	1.0
	C	A:TYR598	4.0	25.1	1.0
	CA	A:ARG600	4.1	33.6	1.0
	CA	A:TYR598	4.1	22.0	1.0
	CG	A:GLU599	4.2	56.8	1.0
	O4	A:SO4705	4.5	45.5	1.0
	C	A:GLU599	4.6	31.1	1.0
	O	A:TYR598	4.6	33.3	1.0
	CA	A:GLU599	4.7	38.0	1.0
	C	A:ARG600	4.9	36.1	1.0
	N	A:TYR598	4.9	20.8	1.0
	CZ	A:PHE601	4.9	37.6	1.0

Reference:

D.W.Robbins, M.A.Noviski. Discovery and Preclinical Pharmacology of Nx-2127, An Orally Bioavailable Degrader of Brutons Tyrosine Kinase with Immunomodulatory Activity For the Treatment of Patients with B Cell Malignancies To Be Published.

Page generated: Wed Oct 9 13:47:57 2024

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