Chlorine in PDB 4mw6: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476), PDB code: 4mw6 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 / 2.56
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	87.277, 106.135, 207.057, 90.00, 90.00, 90.00
*R / R_free (%)*	20.1 / 24.1

Other elements in 4mw6:

Arsenic

(As)

4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476) (pdb code 4mw6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476), PDB code: 4mw6:

Chlorine binding site 1 out of 1 in 4mw6

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Chlorine Binding Sites List in 4mw6

Chlorine binding site 1 out of 1 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl806 b:47.3 occ:1.00	CL	B:2EE806	0.0	47.3	1.0
	C5	B:2EE806	1.7	54.1	1.0
	C4	B:2EE806	2.7	54.3	1.0
	C6	B:2EE806	2.7	57.5	1.0
	OH	B:TYR481	3.5	27.9	1.0
	N	B:ILE248	3.7	30.6	1.0
	CE1	B:HIS523	3.7	39.6	1.0
	CG1	B:ILE248	3.9	31.8	1.0
	CA	B:PRO247	4.0	29.8	1.0
	C3	B:2EE806	4.0	56.1	1.0
	C7	B:2EE806	4.0	63.3	1.0
	NE2	B:HIS523	4.2	38.6	1.0
	CB	B:PRO247	4.2	30.1	1.0
	CZ	B:TYR481	4.2	28.3	1.0
	ND2	B:ASN480	4.3	32.5	1.0
	C	B:PRO247	4.4	30.3	1.0
	O	B:ILE248	4.4	34.2	1.0
	C8	B:2EE806	4.5	60.4	1.0
	O	B:ALA477	4.6	32.1	1.0
	CB	B:ALA477	4.6	33.6	1.0
	CE2	B:TYR481	4.7	28.7	1.0
	CD2	B:LEU478	4.7	33.8	1.0
	CA	B:ILE248	4.7	31.7	1.0
	C	B:ALA477	4.7	33.0	1.0
	CD1	B:ILE519	4.8	33.9	1.0
	CD1	B:ILE248	4.8	31.7	1.0
	CB	B:ILE248	4.8	32.2	1.0
	ND1	B:HIS523	4.9	39.6	1.0
	N	B:LEU478	5.0	32.6	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 21 20:15:44 2024

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