Chlorine in PDB 8un5: Kras-G13D-Gdp in Complex with CPD38 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One)

Enzymatic activity of Kras-G13D-Gdp in Complex with CPD38 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One)

All present enzymatic activity of Kras-G13D-Gdp in Complex with CPD38 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One):
3.6.5.2;

Protein crystallography data

The structure of Kras-G13D-Gdp in Complex with CPD38 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One), PDB code: 8un5 was solved by M.H.Ultsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	31.19 / 1.31
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	38.96, 41.62, 55.55, 90.17, 91.35, 116.28
*R / R_free (%)*	17.8 / 21.2

Other elements in 8un5:

The structure of Kras-G13D-Gdp in Complex with CPD38 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One) also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Fluorine	(F)	8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Kras-G13D-Gdp in Complex with CPD38 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One) (pdb code 8un5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Kras-G13D-Gdp in Complex with CPD38 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One), PDB code: 8un5:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8un5

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Chlorine Binding Sites List in 8un5

Chlorine binding site 1 out of 2 in the Kras-G13D-Gdp in Complex with CPD38 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Kras-G13D-Gdp in Complex with CPD38 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl305 b:14.8 occ:1.00	CL56	A:XQ6305	0.0	14.8	1.0
	C13	A:XQ6305	1.7	13.9	1.0
	C12	A:XQ6305	2.7	12.8	1.0
	C14	A:XQ6305	2.7	13.6	1.0
	H62	A:XQ6305	2.9	16.4	1.0
	C6	A:XQ6305	3.0	13.1	1.0
	O	A:HOH474	3.4	23.8	1.0
	NH1	A:ARG68	3.4	20.1	1.0
	N5	A:XQ6305	3.5	13.3	1.0
	F11	A:XQ6305	3.5	13.5	1.0
	SD	A:MET72	3.5	22.0	0.5
	SD	A:MET72	3.6	21.1	0.5
	C7	A:XQ6305	3.7	13.6	1.0
	CE	A:MET72	3.8	19.1	0.5
	NE	A:ARG68	3.9	21.2	1.0
	CZ	A:ARG68	3.9	19.3	1.0
	C17	A:XQ6305	4.0	12.6	1.0
	C15	A:XQ6305	4.0	13.4	1.0
	CG	A:MET72	4.1	20.3	0.5
	CG2	A:THR58	4.1	14.0	1.0
	CG	A:MET72	4.1	14.7	0.5
	C8	A:XQ6305	4.1	14.5	1.0
	O	A:HOH501	4.2	25.7	1.0
	CB	A:THR58	4.3	12.3	1.0
	C4	A:XQ6305	4.4	13.0	1.0
	C16	A:XQ6305	4.5	12.3	1.0
	F10	A:XQ6305	4.6	15.0	1.0
	H70	A:XQ6305	4.6	19.9	1.0
	C2	A:XQ6305	4.6	13.7	1.0
	H29	A:XQ6305	4.7	18.7	1.0
	OG1	A:THR58	4.7	10.1	1.0
	O	A:HOH485	4.8	12.7	1.0
	H69	A:XQ6305	4.8	19.9	1.0
	CE	A:MET72	4.8	33.3	0.5
	C3	A:XQ6305	4.9	13.1	1.0

Chlorine binding site 2 out of 2 in 8un5

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Chlorine Binding Sites List in 8un5

Chlorine binding site 2 out of 2 in the Kras-G13D-Gdp in Complex with CPD38 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Kras-G13D-Gdp in Complex with CPD38 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl203 b:15.0 occ:1.00	CL56	B:XQ6203	0.0	15.0	1.0
	C13	B:XQ6203	1.7	14.1	1.0
	C14	B:XQ6203	2.7	13.6	1.0
	C12	B:XQ6203	2.7	12.8	1.0
	H62	B:XQ6203	2.8	16.3	1.0
	C6	B:XQ6203	3.1	13.5	1.0
	O	B:HOH352	3.4	24.9	1.0
	NH1	B:ARG68	3.4	15.9	1.0
	F11	B:XQ6203	3.5	15.1	1.0
	N5	B:XQ6203	3.5	13.6	1.0
	SD	B:MET72	3.6	21.1	1.0
	C7	B:XQ6203	3.8	13.8	1.0
	NE	B:ARG68	3.9	18.9	1.0
	CZ	B:ARG68	4.0	17.3	1.0
	C17	B:XQ6203	4.0	14.6	1.0
	C15	B:XQ6203	4.0	13.4	1.0
	CG	B:MET72	4.0	16.6	1.0
	O	B:HOH405	4.1	26.2	1.0
	CG2	B:THR58	4.2	16.0	1.0
	C8	B:XQ6203	4.2	15.5	1.0
	CB	B:THR58	4.2	11.1	1.0
	CE	B:MET72	4.4	27.3	1.0
	C4	B:XQ6203	4.5	13.9	1.0
	C16	B:XQ6203	4.5	13.8	1.0
	F10	B:XQ6203	4.6	17.4	1.0
	H29	B:XQ6203	4.6	21.7	1.0
	H70	B:XQ6203	4.6	23.3	1.0
	O	B:HOH383	4.7	14.5	1.0
	OG1	B:THR58	4.7	10.1	1.0
	C2	B:XQ6203	4.7	13.1	1.0
	H69	B:XQ6203	4.8	23.3	1.0
	C3	B:XQ6203	5.0	13.4	1.0

Reference:

C.Nilewski, M.H.Ultsch. N/A N/A.

Page generated: Thu Dec 28 03:36:21 2023

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