Chlorine in PDB 7ebh: Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 13

Enzymatic activity of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 13

All present enzymatic activity of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 13:
2.7.11.2;

Protein crystallography data

The structure of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 13, PDB code: 7ebh was solved by T.Orita, S.Doi, T.Iwanaga, T.Adachi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	94.70 / 1.96
*Space group*	P 6₄
*Cell size a, b, c (Å), α, β, γ (°)*	109.347, 109.347, 84.167, 90, 90, 120
*R / R_free (%)*	19.9 / 20.2

Other elements in 7ebh:

The structure of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 13 also contains other interesting chemical elements:

Bromine

(Br)

1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 13 (pdb code 7ebh). 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 Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 13, PDB code: 7ebh:

Chlorine binding site 1 out of 1 in 7ebh

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Chlorine Binding Sites List in 7ebh

Chlorine binding site 1 out of 1 in the Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 13

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Pyruvate Dehydrogenase Kinase 2 in Complex with Compound 13 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl501 b:49.4 occ:1.00	OH	A:TYR88	2.8	42.6	1.0
	O	A:ACT503	3.2	48.8	1.0
	NE	A:ARG162	3.2	51.3	1.0
	CD	A:ARG162	3.3	51.0	1.0
	CG	A:ARG162	3.4	45.5	1.0
	ND1	A:HIS123	3.5	49.9	1.0
	CZ	A:TYR88	3.5	46.0	1.0
	CG2	A:VAL126	3.5	52.4	1.0
	CE1	A:TYR88	3.6	41.6	1.0
	CG1	A:VAL126	3.6	51.0	1.0
	CH3	A:ACT503	3.6	49.6	1.0
	CB	A:VAL126	3.8	48.6	1.0
	C	A:ACT503	3.9	53.7	1.0
	CB	A:HIS123	3.9	51.8	1.0
	CB	A:ARG162	3.9	34.8	1.0
	CG	A:HIS123	4.1	51.1	1.0
	CZ	A:PHE158	4.2	42.1	1.0
	CZ	A:ARG162	4.4	50.1	1.0
	CE1	A:HIS123	4.6	53.8	1.0
	O	A:HIS123	4.6	48.1	1.0
	CE2	A:PHE158	4.7	42.6	1.0
	CA	A:ARG162	4.7	35.5	1.0
	CE2	A:TYR88	4.7	45.1	1.0
	O	A:HOH609	4.8	43.2	1.0
	CD1	A:TYR88	4.8	46.0	1.0
	NH2	A:ARG162	4.8	50.8	1.0
	CE1	A:PHE158	4.9	43.1	1.0

Reference:

T.Akaki, Y.Bessho, T.Ito, S.Fujioka, M.Ubukata, G.Mori, K.Yamanaka, T.Orita, S.Doi, T.Iwanaga, K.Ikegashira, Y.Hantani, I.Nakanishi, T.Adachi. Fragment-Based Lead Discovery to Identify Novel Inhibitors That Target the Atp Binding Site of Pyruvate Dehydrogenase Kinases. Bioorg.Med.Chem. V. 44 16283 2021.
ISSN: ESSN 1464-3391
PubMed: 34274549
DOI: 10.1016/J.BMC.2021.116283

Page generated: Sun Jul 13 00:21:31 2025

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