Sodium in PDB 5iw8: Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 4 [5-(3-([1,1'-Biphenyl]-3-Yl)Ureido)-2-Hydroxybenzoic Acid]

Enzymatic activity of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 4 [5-(3-([1,1'-Biphenyl]-3-Yl)Ureido)-2-Hydroxybenzoic Acid]

All present enzymatic activity of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 4 [5-(3-([1,1'-Biphenyl]-3-Yl)Ureido)-2-Hydroxybenzoic Acid]:
2.5.1.113;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 4 [5-(3-([1,1'-Biphenyl]-3-Yl)Ureido)-2-Hydroxybenzoic Acid], PDB code: 5iw8 was solved by K.Brunner, R.Schnell, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	55.95 / 2.04
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	67.164, 87.883, 100.781, 90.00, 90.00, 90.00
*R / R_free (%)*	18.4 / 23.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 4 [5-(3-([1,1'-Biphenyl]-3-Yl)Ureido)-2-Hydroxybenzoic Acid] (pdb code 5iw8). 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 Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 4 [5-(3-([1,1'-Biphenyl]-3-Yl)Ureido)-2-Hydroxybenzoic Acid], PDB code: 5iw8:

Sodium binding site 1 out of 1 in 5iw8

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Sodium Binding Sites List in 5iw8

Sodium binding site 1 out of 1 in the Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 4 [5-(3-([1,1'-Biphenyl]-3-Yl)Ureido)-2-Hydroxybenzoic Acid]

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mycobacterium Tuberculosis Cysm in Complex with the Urea-Scaffold Inhibitor 4 [5-(3-([1,1'-Biphenyl]-3-Yl)Ureido)-2-Hydroxybenzoic Acid] within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na402 b:41.2 occ:1.00	O	A:ASN143	2.2	36.9	1.0
	O	A:HOH654	2.3	28.1	1.0
	O	A:ALA140	2.4	34.8	1.0
	O	A:HOH603	2.4	37.1	1.0
	O	A:TRP146	2.5	29.6	1.0
	C	A:ASN143	3.2	38.8	1.0
	C	A:ALA140	3.3	31.0	1.0
	C	A:TRP146	3.6	32.3	1.0
	O	A:PRO144	3.8	48.3	1.0
	CA	A:PRO144	3.8	42.0	1.0
	N	A:PRO144	3.9	41.5	1.0
	C	A:PRO144	4.0	40.4	1.0
	O	A:HOH667	4.0	45.0	1.0
	N	A:ALA141	4.1	32.1	1.0
	CA	A:ALA140	4.2	29.5	1.0
	N	A:TRP146	4.2	34.0	1.0
	N	A:ASN143	4.2	35.8	1.0
	CA	A:ALA141	4.2	33.4	1.0
	CB	A:ALA140	4.3	30.0	1.0
	CA	A:TRP146	4.3	31.4	1.0
	CA	A:ASN143	4.3	38.1	1.0
	CB	A:TRP146	4.4	31.5	1.0
	C	A:ALA141	4.6	32.2	1.0
	N	A:VAL147	4.7	29.0	1.0
	N	A:SER145	4.8	37.5	1.0
	O	A:ALA141	4.9	30.2	1.0
	O	A:HOH604	4.9	31.7	1.0

Reference:

K.Brunner, S.Maric, R.S.Reshma, H.Almqvist, B.Seashore-Ludlow, A.L.Gustavsson, O.Poyraz, P.Yogeeswari, T.Lundback, M.Vallin, D.Sriram, R.Schnell, G.Schneider. Inhibitors of the Cysteine Synthase Cysm with Antibacterial Potency Against Dormant Mycobacterium Tuberculosis. J.Med.Chem. V. 59 6848 2016.
ISSN: ISSN 0022-2623
PubMed: 27379713
DOI: 10.1021/ACS.JMEDCHEM.6B00674

Page generated: Mon Aug 18 00:22:53 2025

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