Fluorine in PDB 6hu3: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor, PDB code: 6hu3 was solved by T.B.Shaik, M.Marek, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	48.95 / 1.66
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	70.640, 70.430, 97.920, 75.48, 78.20, 86.17
*R / R_free (%)*	16.2 / 19.4

Other elements in 6hu3:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor also contains other interesting chemical elements:

Potassium	(K)	8 atoms
Zinc	(Zn)	4 atoms
Chlorine	(Cl)	4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor (pdb code 6hu3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor, PDB code: 6hu3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6hu3

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Fluorine Binding Sites List in 6hu3

Fluorine binding site 1 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F504 b:68.5 occ:1.00	F1	A:GRZ504	0.0	68.5	1.0
	C1	A:GRZ504	1.4	59.3	1.0
	C2	A:GRZ504	2.3	57.9	1.0
	C6	A:GRZ504	2.3	54.2	1.0
	CG	A:PRO291	3.3	39.6	1.0
	C3	A:GRZ504	3.6	55.7	1.0
	C5	A:GRZ504	3.6	55.2	1.0
	CB	A:PRO291	3.6	39.7	1.0
	CB	A:TYR341	4.1	35.0	1.0
	C4	A:GRZ504	4.1	55.1	1.0
	CG	A:TYR341	4.7	45.7	1.0
	CD	A:PRO291	4.8	31.2	1.0
	CA	A:PRO291	4.9	35.9	1.0

Fluorine binding site 2 out of 4 in 6hu3

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Fluorine Binding Sites List in 6hu3

Fluorine binding site 2 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:F504 b:52.1 occ:1.00	F1	B:GRZ504	0.0	52.1	1.0
	C1	B:GRZ504	1.4	57.7	1.0
	C2	B:GRZ504	2.3	54.7	1.0
	C6	B:GRZ504	2.4	55.8	1.0
	CG	B:PRO291	3.2	29.1	1.0
	CB	B:PRO291	3.6	30.8	1.0
	C3	B:GRZ504	3.6	54.2	1.0
	C5	B:GRZ504	3.6	51.6	1.0
	O	B:HOH837	3.9	58.0	1.0
	CB	B:TYR341	4.1	35.8	1.0
	C4	B:GRZ504	4.1	54.5	1.0
	CD	B:PRO291	4.7	25.3	1.0
	CG	B:TYR341	4.7	42.4	1.0
	NZ	B:LYS20	4.8	83.9	1.0
	CA	B:PRO291	4.9	28.6	1.0

Fluorine binding site 3 out of 4 in 6hu3

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Fluorine Binding Sites List in 6hu3

Fluorine binding site 3 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:F504 b:59.1 occ:1.00	F1	C:GRZ504	0.0	59.1	1.0
	C1	C:GRZ504	1.4	57.1	1.0
	C6	C:GRZ504	2.3	55.4	1.0
	C2	C:GRZ504	2.4	53.6	1.0
	CG	C:PRO291	3.2	31.3	1.0
	CB	C:PRO291	3.5	29.9	1.0
	C5	C:GRZ504	3.6	55.4	1.0
	C3	C:GRZ504	3.6	52.7	1.0
	O	C:HOH820	4.0	54.8	1.0
	C4	C:GRZ504	4.1	52.3	1.0
	CB	C:TYR341	4.1	31.7	1.0
	CD	C:PRO291	4.7	28.5	1.0
	CG	C:TYR341	4.8	41.5	1.0
	NZ	C:LYS20	4.8	79.7	1.0
	CA	C:PRO291	4.9	28.9	1.0

Fluorine binding site 4 out of 4 in 6hu3

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Fluorine Binding Sites List in 6hu3

Fluorine binding site 4 out of 4 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Triazole Hydroxamate Inhibitor within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:F504 b:74.8 occ:1.00	F1	D:GRZ504	0.0	74.8	1.0
	C1	D:GRZ504	1.4	69.8	1.0
	C2	D:GRZ504	2.3	68.4	1.0
	C6	D:GRZ504	2.3	70.0	1.0
	CG	D:PRO291	3.3	40.7	1.0
	CB	D:PRO291	3.4	35.5	1.0
	C3	D:GRZ504	3.6	68.5	1.0
	C5	D:GRZ504	3.6	69.8	1.0
	C4	D:GRZ504	4.1	71.1	1.0
	CB	D:TYR341	4.5	37.6	1.0
	O	D:HOH792	4.5	59.3	1.0
	CA	D:PRO291	4.7	34.1	1.0
	CD	D:PRO291	4.8	40.1	1.0
	C	D:PRO291	4.9	35.5	1.0

Reference:

M.Marek, T.B.Shaik, T.Heimburg, A.Chakrabarti, J.Lancelot, E.Ramos-Morales, C.Da Veiga, D.Kalinin, J.Melesina, D.Robaa, K.Schmidtkunz, T.Suzuki, R.Holl, E.Ennifar, R.J.Pierce, M.Jung, W.Sippl, C.Romier. Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. J. Med. Chem. V. 61 10000 2018.
ISSN: ISSN 1520-4804
PubMed: 30347148
DOI: 10.1021/ACS.JMEDCHEM.8B01087

Page generated: Thu Aug 1 21:19:38 2024

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