Iodine in PDB 4mw4: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Hydroxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1473)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Hydroxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1473)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Hydroxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1473):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Hydroxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1473), PDB code: 4mw4 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 / 2.50
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	87.829, 106.063, 207.642, 90.00, 90.00, 90.00
*R / R_free (%)*	20.4 / 23.1

Other elements in 4mw4:

Arsenic	(As)	2 atoms
Chlorine	(Cl)	1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Hydroxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1473) (pdb code 4mw4). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total only one binding site of Iodine was determined in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Hydroxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1473), PDB code: 4mw4:

Iodine binding site 1 out of 1 in 4mw4

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Iodine Binding Sites List in 4mw4

Iodine binding site 1 out of 1 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Hydroxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1473)

Mono view

Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Hydroxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1473) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:I810 b:33.1 occ:1.00	I	B:2EB810	0.0	33.1	1.0
	C14	B:2EB810	2.1	34.6	1.0
	C13	B:2EB810	3.1	35.4	1.0
	C	B:2EB810	3.1	35.6	1.0
	O	B:2EB810	3.3	37.7	1.0
	OH	B:TYR481	3.4	21.9	1.0
	NE2	B:HIS523	3.7	24.6	1.0
	N	B:ILE248	3.8	24.9	1.0
	CE1	B:HIS523	3.8	24.7	1.0
	ND2	B:ASN480	3.9	25.3	1.0
	CZ	B:TYR481	4.0	22.4	1.0
	CG1	B:ILE248	4.0	24.7	1.0
	CA	B:PRO247	4.1	24.8	1.0
	CB	B:PRO247	4.2	25.5	1.0
	C12	B:2EB810	4.4	35.7	1.0
	CD2	B:LEU478	4.4	25.5	1.0
	CE2	B:TYR481	4.4	22.2	1.0
	O	B:ALA477	4.4	25.8	1.0
	C1	B:2EB810	4.4	36.3	1.0
	CB	B:ALA477	4.5	26.7	1.0
	C	B:PRO247	4.5	24.9	1.0
	C	B:ALA477	4.5	25.9	1.0
	O	B:ILE248	4.6	25.1	1.0
	N	B:LEU478	4.7	25.2	1.0
	CA	B:LEU478	4.7	25.1	1.0
	CE1	B:TYR481	4.8	22.9	1.0
	CA	B:ILE248	4.9	24.6	1.0
	CD1	B:ILE248	4.9	25.1	1.0
	C11	B:2EB810	4.9	35.1	1.0
	CB	B:ILE248	4.9	24.6	1.0
	CD1	B:ILE519	5.0	27.8	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: Fri Aug 8 17:57:58 2025

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