Manganese in PDB 5wdy: Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6)

Enzymatic activity of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6)

All present enzymatic activity of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6):
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6), PDB code: 5wdy was solved by X.Xie, D.Kohls, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	32.84 / 2.46
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	34.334, 62.267, 70.268, 67.13, 77.42, 74.74
*R / R_free (%)*	22.8 / 28.5

Other elements in 5wdy:

Fluorine

(F)

2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6) (pdb code 5wdy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6), PDB code: 5wdy:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5wdy

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Manganese Binding Sites List in 5wdy

Manganese binding site 1 out of 3 in the Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6)

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn903 b:86.9 occ:1.00	O	A:HOH1007	2.9	73.6	1.0
	O	A:HOH1003	4.1	46.5	1.0
	O	A:GLU466	4.3	55.3	1.0
	CG	A:TYR468	4.3	49.0	1.0
	CD1	A:TYR468	4.3	50.9	1.0
	CA	A:TYR468	4.4	46.0	1.0
	CD2	A:TYR468	4.4	50.6	1.0
	N	A:TYR468	4.4	51.4	1.0
	CE1	A:TYR468	4.4	57.8	1.0
	CE2	A:TYR468	4.5	53.2	1.0
	CZ	A:TYR468	4.5	57.5	1.0
	C	A:ARG467	4.5	45.7	1.0
	O	A:ARG467	4.6	46.5	1.0
	NH1	A:ARG461	4.6	66.9	1.0
	CB	A:TYR468	4.9	48.3	1.0

Manganese binding site 2 out of 3 in 5wdy

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Manganese Binding Sites List in 5wdy

Manganese binding site 2 out of 3 in the Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6)

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn904 b:0.4 occ:1.00	OD1	A:ASN354	2.4	65.5	1.0
	OD2	A:ASP368	2.4	77.4	1.0
	O	A:HOH1005	2.5	70.5	1.0
	O1A	A:ANP901	2.6	0.1	1.0
	O2A	A:ANP901	2.8	0.7	1.0
	PA	A:ANP901	3.1	0.5	1.0
	CG	A:ASP368	3.3	68.1	1.0
	CG	A:ASN354	3.4	55.0	1.0
	CB	A:ASP368	3.8	53.8	1.0
	ND2	A:ASN354	3.8	51.7	1.0
	O3A	A:ANP901	3.9	0.5	1.0
	O2G	A:ANP901	4.0	0.8	1.0
	NZ	A:LYS233	4.3	0.2	1.0
	OD1	A:ASP368	4.3	61.4	1.0
	N3B	A:ANP901	4.4	0.8	1.0
	O5'	A:ANP901	4.5	0.9	1.0
	CB	A:ASN354	4.7	50.9	1.0
	O	A:ASP353	4.7	56.4	1.0
	PG	A:ANP901	4.7	1.0	1.0
	PB	A:ANP901	4.9	0.4	1.0
	OD1	A:ASP349	4.9	53.6	1.0
	CA	A:ASN354	4.9	50.5	1.0
	CE	A:LYS351	5.0	61.7	1.0

Manganese binding site 3 out of 3 in 5wdy

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Manganese Binding Sites List in 5wdy

Manganese binding site 3 out of 3 in the Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6)

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of WNK1 in Complex with 1-Cyclohexyl-N-({6-Fluoro-1- [2-(3-Methoxyphenyl)Pyridin-4-Yl]-1H-Indol-3-Yl}Methyl)Methanamine (Compound 6) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn501 b:0.8 occ:1.00	O1G	B:ANP502	2.3	0.9	1.0
	O2A	B:ANP502	2.4	0.7	1.0
	OD1	B:ASN354	2.5	70.1	1.0
	OD2	B:ASP368	3.1	80.2	1.0
	PG	B:ANP502	3.5	0.1	1.0
	CG	B:ASP368	3.5	74.2	1.0
	CG	B:ASN354	3.6	61.5	1.0
	PA	B:ANP502	3.6	0.9	1.0
	O3G	B:ANP502	3.7	0.6	1.0
	O2B	B:ANP502	3.7	0.9	1.0
	O3A	B:ANP502	3.8	0.4	1.0
	CB	B:ASP368	3.9	63.1	1.0
	PB	B:ANP502	4.2	0.3	1.0
	ND2	B:ASN354	4.2	63.9	1.0
	O	B:ASP353	4.2	63.1	1.0
	N3B	B:ANP502	4.3	0.4	1.0
	OD1	B:ASP368	4.3	70.2	1.0
	O1A	B:ANP502	4.4	0.1	1.0
	CA	B:ASN354	4.6	55.0	1.0
	CB	B:ASN354	4.6	54.5	1.0
	C	B:ASP353	4.7	55.8	1.0
	O2G	B:ANP502	4.7	0.3	1.0
	N	B:ASN354	4.7	55.3	1.0
	NZ	B:LYS233	4.8	85.8	1.0
	O5'	B:ANP502	4.9	97.6	1.0

Reference:

K.Yamada, J.Levell, T.Yoon, D.Kohls, D.Yowe, D.F.Rigel, H.Imase, J.Yuan, K.Yasoshima, K.Dipetrillo, L.Monovich, L.Xu, M.Zhu, M.Kato, M.Jain, N.Idamakanti, P.Taslimi, T.Kawanami, U.A.Argikar, V.Kunjathoor, X.Xie, Y.I.Yagi, Y.Iwaki, Z.Robinson, H.M.Park. Optimization of Allosteric with-No-Lysine (Wnk) Kinase Inhibitors and Efficacy in Rodent Hypertension Models. J. Med. Chem. V. 60 7099 2017.
ISSN: ISSN 1520-4804
PubMed: 28771350
DOI: 10.1021/ACS.JMEDCHEM.7B00708

Page generated: Sun Oct 6 03:19:37 2024

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