Arsenic in PDB 4mw5: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3-Chloro-5-Methoxybenzyl)Amino]Propyl}-3-Phenylurea (Chem 1415)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3-Chloro-5-Methoxybenzyl)Amino]Propyl}-3-Phenylurea (Chem 1415)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3-Chloro-5-Methoxybenzyl)Amino]Propyl}-3-Phenylurea (Chem 1415):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3-Chloro-5-Methoxybenzyl)Amino]Propyl}-3-Phenylurea (Chem 1415), PDB code: 4mw5 was solved by C.Y.Koh, J.E.Kim, A.B.Wetzel, W.J.De Van Der Schueren, S.Shibata, J.Liu, Z.Zhang, E.Fan, C.L.M.J.Verlinde, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	30.00 / 2.35
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	87.449, 105.728, 206.592, 90.00, 90.00, 90.00
*R / R_free (%)*	18.9 / 21.7

Other elements in 4mw5:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3-Chloro-5-Methoxybenzyl)Amino]Propyl}-3-Phenylurea (Chem 1415) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3-Chloro-5-Methoxybenzyl)Amino]Propyl}-3-Phenylurea (Chem 1415) (pdb code 4mw5). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3-Chloro-5-Methoxybenzyl)Amino]Propyl}-3-Phenylurea (Chem 1415), PDB code: 4mw5:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4mw5

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Arsenic Binding Sites List in 4mw5

Arsenic binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3-Chloro-5-Methoxybenzyl)Amino]Propyl}-3-Phenylurea (Chem 1415)

Mono view

Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3-Chloro-5-Methoxybenzyl)Amino]Propyl}-3-Phenylurea (Chem 1415) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:As470 b:34.4 occ:0.30	AS	A:CAS470	0.0	34.4	0.3
	CE2	A:CAS470	2.0	36.1	0.3
	CE1	A:CAS470	2.0	35.7	0.3
	SG	A:CAS470	2.2	38.3	1.0
	CB	A:CAS470	3.0	32.8	1.0
	CA	A:CAS470	3.5	30.3	1.0
	O	A:ALA460	3.6	30.4	1.0
	CA	A:PRO462	3.7	29.0	1.0
	N	A:PRO462	3.7	29.1	1.0
	C	A:ILE461	3.9	28.6	1.0
	O	A:ILE461	3.9	28.0	1.0
	C	A:ALA460	4.0	29.6	1.0
	O	A:HIS469	4.0	30.1	1.0
	N	A:CAS470	4.1	30.6	1.0
	CG	A:PRO462	4.2	30.9	1.0
	CB	A:ALA460	4.2	29.3	1.0
	CB	A:PRO462	4.3	30.1	1.0
	CD	A:PRO462	4.3	30.1	1.0
	C	A:HIS469	4.3	30.6	1.0
	N	A:ILE461	4.4	28.5	1.0
	CB	A:ARG453	4.5	36.4	1.0
	CA	A:ALA460	4.5	29.8	1.0
	N	A:ALA460	4.7	31.9	1.0
	CA	A:ILE461	4.7	28.8	1.0
	CA	A:ASN458	4.9	42.9	1.0
	C	A:CAS470	4.9	28.1	1.0
	C	A:PRO462	5.0	27.8	1.0
	C	A:ASN458	5.0	40.8	1.0

Arsenic binding site 2 out of 2 in 4mw5

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Arsenic Binding Sites List in 4mw5

Arsenic binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3-Chloro-5-Methoxybenzyl)Amino]Propyl}-3-Phenylurea (Chem 1415)

Mono view

Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3-Chloro-5-Methoxybenzyl)Amino]Propyl}-3-Phenylurea (Chem 1415) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:As470 b:35.2 occ:0.30	AS	B:CAS470	0.0	35.2	0.3
	CE1	B:CAS470	1.9	34.8	0.3
	CE2	B:CAS470	2.0	36.0	0.3
	SG	B:CAS470	2.2	32.8	1.0
	O	B:ALA460	3.1	27.6	1.0
	CB	B:CAS470	3.2	30.4	1.0
	C	B:ALA460	3.6	26.5	1.0
	C	B:ILE461	3.9	25.4	1.0
	O	B:ILE461	4.0	24.6	1.0
	CA	B:CAS470	4.0	28.9	1.0
	N	B:PRO462	4.0	26.6	1.0
	CB	B:ALA460	4.0	26.4	1.0
	CA	B:ALA460	4.1	26.6	1.0
	N	B:ALA460	4.2	27.1	1.0
	CA	B:PRO462	4.2	27.0	1.0
	N	B:ILE461	4.2	25.4	1.0
	CB	B:ARG453	4.4	32.2	1.0
	CD	B:PRO462	4.5	27.7	1.0
	C	B:ASN458	4.5	33.0	1.0
	O	B:ASN458	4.5	33.8	1.0
	CA	B:ILE461	4.6	25.4	1.0
	N	B:CAS470	4.6	29.2	1.0
	O	B:HIS469	4.6	30.1	1.0
	CA	B:ASN458	4.6	34.6	1.0
	CG	B:PRO462	4.7	28.6	1.0
	O1	B:GOL903	4.7	56.8	1.0
	CB	B:PRO462	4.7	27.9	1.0
	C	B:HIS469	4.8	30.3	1.0
	CA	B:ARG453	4.9	30.7	1.0
	N	B:TRP459	5.0	30.4	1.0

Reference:

C.Y.Koh, J.E.Kim, A.B.Wetzel, W.J.De Van Der Schueren, S.Shibata, R.M.Ranade, J.Liu, Z.Zhang, J.R.Gillespie, F.S.Buckner, C.L.Verlinde, E.Fan, W.G.Hol. Structures of Trypanosoma Brucei Methionyl-Trna Synthetase with Urea-Based Inhibitors Provide Guidance For Drug Design Against Sleeping Sickness. Plos Negl Trop Dis V. 8 E2775 2014.
ISSN: ISSN 1935-2727
PubMed: 24743796
DOI: 10.1371/JOURNAL.PNTD.0002775

Page generated: Sun Jul 6 23:52:24 2025

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