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Fluorine in PDB 7rt1: Crystal Structure of Kras G12D with Compound 15 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S)-1-Methylpyrrolidin- 2-Yl]Methoxy}Pyrido[4,3-D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound

Enzymatic activity of Crystal Structure of Kras G12D with Compound 15 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S)-1-Methylpyrrolidin- 2-Yl]Methoxy}Pyrido[4,3-D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound

All present enzymatic activity of Crystal Structure of Kras G12D with Compound 15 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S)-1-Methylpyrrolidin- 2-Yl]Methoxy}Pyrido[4,3-D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Kras G12D with Compound 15 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S)-1-Methylpyrrolidin- 2-Yl]Methoxy}Pyrido[4,3-D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound, PDB code: 7rt1 was solved by R.G.Gunn, N.C.Thomas, W.Xiaolun, J.D.Lawson, M.A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.92 / 1.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.733, 51.839, 89.84, 90, 90, 90
R / Rfree (%) 13.5 / 16.8

Other elements in 7rt1:

The structure of Crystal Structure of Kras G12D with Compound 15 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S)-1-Methylpyrrolidin- 2-Yl]Methoxy}Pyrido[4,3-D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Kras G12D with Compound 15 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S)-1-Methylpyrrolidin- 2-Yl]Methoxy}Pyrido[4,3-D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound (pdb code 7rt1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Kras G12D with Compound 15 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S)-1-Methylpyrrolidin- 2-Yl]Methoxy}Pyrido[4,3-D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound, PDB code: 7rt1:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7rt1

Go back to Fluorine Binding Sites List in 7rt1
Fluorine binding site 1 out of 2 in the Crystal Structure of Kras G12D with Compound 15 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S)-1-Methylpyrrolidin- 2-Yl]Methoxy}Pyrido[4,3-D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound


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 Kras G12D with Compound 15 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S)-1-Methylpyrrolidin- 2-Yl]Methoxy}Pyrido[4,3-D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:7.7
occ:1.00
 F28 A:7L8203 0.0 7.7 1.0
C11 A:7L8203 1.4 7.1 1.0
C3 A:7L8203 2.3 6.5 1.0
C2 A:7L8203 2.4 7.3 1.0
N6 A:7L8203 2.7 6.7 1.0
C10 A:7L8203 2.8 7.5 1.0
C37 A:7L8203 3.1 6.9 1.0
C33 A:7L8203 3.1 7.5 1.0
NE2 A:HIS95 3.1 8.4 1.0
CE2 A:TYR64 3.3 10.0 1.0
OH A:TYR64 3.4 10.6 1.0
CG A:GLN99 3.4 7.5 1.0
C4 A:7L8203 3.6 6.1 1.0
N1 A:7L8203 3.6 7.5 1.0
CZ A:TYR64 3.7 9.3 1.0
C29 A:7L8203 3.8 7.6 1.0
CD2 A:HIS95 3.9 7.9 1.0
CE1 A:HIS95 4.0 8.0 1.0
CB A:GLN99 4.0 7.5 1.0
C7 A:7L8203 4.0 6.6 1.0
C5 A:7L8203 4.0 7.5 1.0
C36 A:7L8203 4.1 7.4 1.0
C32 A:7L8203 4.3 7.7 1.0
CE1 A:TYR96 4.3 7.3 1.0
CD A:GLN99 4.3 8.1 1.0
CD1 A:TYR96 4.4 7.3 1.0
CD2 A:TYR64 4.4 10.3 1.0
OE1 A:GLN99 4.6 9.1 1.0
C9 A:7L8203 4.7 6.9 1.0
O12 A:7L8203 4.8 7.1 1.0
C30 A:7L8203 4.8 8.8 1.0
O A:HOH506 4.9 12.0 1.0
N8 A:7L8203 4.9 6.9 1.0
ND1 A:HIS95 4.9 7.3 1.0
CG A:HIS95 5.0 7.1 1.0
CE1 A:TYR64 5.0 9.2 1.0
C31 A:7L8203 5.0 8.2 1.0

Fluorine binding site 2 out of 2 in 7rt1

Go back to Fluorine Binding Sites List in 7rt1
Fluorine binding site 2 out of 2 in the Crystal Structure of Kras G12D with Compound 15 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S)-1-Methylpyrrolidin- 2-Yl]Methoxy}Pyrido[4,3-D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound


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 Kras G12D with Compound 15 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S)-1-Methylpyrrolidin- 2-Yl]Methoxy}Pyrido[4,3-D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F204

b:14.5
occ:1.00
 F28 A:7L8204 0.0 14.5 1.0
C11 A:7L8204 1.4 12.0 1.0
C2 A:7L8204 2.3 11.9 1.0
C3 A:7L8204 2.4 11.7 1.0
N6 A:7L8204 2.8 13.3 1.0
C10 A:7L8204 2.8 10.7 1.0
O A:HOH325 3.2 16.6 1.0
CD1 A:LEU56 3.3 7.7 1.0
C29 A:7L8204 3.5 10.8 1.0
C33 A:7L8204 3.6 9.8 1.0
N1 A:7L8204 3.6 15.3 1.0
C4 A:7L8204 3.6 13.7 1.0
CD2 A:LEU56 3.8 9.0 1.0
C37 A:7L8204 3.9 11.1 1.0
C5 A:7L8204 4.0 13.9 1.0
CD1 A:TYR71 4.0 12.4 1.0
C7 A:7L8204 4.0 14.4 1.0
CG A:LEU56 4.1 7.4 1.0
CE1 A:TYR71 4.3 12.1 1.0
O A:HOH480 4.5 24.4 1.0
O A:HOH369 4.5 23.1 1.0
CG A:TYR71 4.5 12.1 1.0
C30 A:7L8204 4.5 9.8 1.0
C32 A:7L8204 4.6 10.2 1.0
OE2 A:GLU37 4.7 12.5 1.0
C9 A:7L8204 4.7 13.3 1.0
O12 A:7L8204 4.8 15.1 1.0
CB A:LEU56 4.8 6.9 1.0
N8 A:7L8204 4.9 13.0 1.0
CZ A:TYR71 5.0 12.1 1.0
CB A:TYR71 5.0 12.5 1.0

Reference:

X.Wang, S.Allen, J.F.Blake, V.Bowcut, D.M.Briere, A.Calinisan, J.R.Dahlke, J.B.Fell, J.P.Fischer, R.J.Gunn, J.Hallin, J.Laguer, J.D.Lawson, J.Medwid, B.Newhouse, P.Nguyen, J.M.O'leary, P.Olson, S.Pajk, L.Rahbaek, M.Rodriguez, C.R.Smith, T.P.Tang, N.C.Thomas, D.Vanderpool, G.P.Vigers, J.G.Christensen, M.A.Marx. Identification of MRTX1133, A Noncovalent, Potent, and Selective Kras G12D Inhibitor. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34889605
DOI: 10.1021/ACS.JMEDCHEM.1C01688
Page generated: Tue Jul 15 23:54:23 2025

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