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Fluorine in PDB 7rt2: Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound

Enzymatic activity of Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-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 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-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 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound, PDB code: 7rt2 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) 45.74 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.96, 52.972, 90.708, 90, 90, 90
R / Rfree (%) 15.7 / 18

Other elements in 7rt2:

The structure of Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-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 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound (pdb code 7rt2). 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 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound, PDB code: 7rt2:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7rt2

Go back to Fluorine Binding Sites List in 7rt2
Fluorine binding site 1 out of 2 in the Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-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 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-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:18.3
occ:1.00
 F12 A:7NL203 0.0 18.3 1.0
C10 A:7NL203 1.4 17.8 1.0
C2 A:7NL203 2.4 14.3 1.0
C9 A:7NL203 2.4 19.3 1.0
N3 A:7NL203 2.7 15.8 1.0
C21 A:7NL203 2.9 16.8 1.0
C36 A:7NL203 3.1 16.7 1.0
NE2 A:HIS95 3.1 18.3 1.0
C31 A:7NL203 3.2 16.7 1.0
CE2 A:TYR64 3.2 18.4 1.0
OH A:TYR64 3.3 18.4 1.0
CG A:GLN99 3.4 16.8 1.0
N8 A:7NL203 3.6 19.9 1.0
C1 A:7NL203 3.6 13.4 1.0
CZ A:TYR64 3.7 19.3 1.0
C35 A:7NL203 3.8 16.8 1.0
CE1 A:HIS95 3.9 19.1 1.0
CD2 A:HIS95 3.9 17.7 1.0
CB A:GLN99 4.0 16.6 1.0
C4 A:7NL203 4.0 17.2 1.0
C7 A:7NL203 4.1 17.5 1.0
C37 A:7NL203 4.2 14.8 1.0
CD2 A:TYR64 4.3 20.5 1.0
CD A:GLN99 4.3 18.2 1.0
C32 A:7NL203 4.3 18.2 1.0
CE1 A:TYR96 4.4 14.5 1.0
OE1 A:GLN99 4.5 21.0 1.0
CD1 A:TYR96 4.5 14.3 1.0
C6 A:7NL203 4.8 15.9 1.0
O11 A:7NL203 4.8 16.2 1.0
O A:HOH348 4.8 21.1 1.0
C34 A:7NL203 4.8 19.1 1.0
ND1 A:HIS95 4.9 18.4 1.0
CE1 A:TYR64 4.9 17.9 1.0
CG A:HIS95 4.9 16.1 1.0
N5 A:7NL203 4.9 15.6 1.0

Fluorine binding site 2 out of 2 in 7rt2

Go back to Fluorine Binding Sites List in 7rt2
Fluorine binding site 2 out of 2 in the Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-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 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-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:19.7
occ:1.00
 F262 A:7NL203 0.0 19.7 1.0
C26 A:7NL203 1.4 17.7 1.0
C25 A:7NL203 2.3 18.2 1.0
C27 A:7NL203 2.4 16.6 1.0
N24 A:7NL203 3.0 16.1 1.0
C23 A:7NL203 3.0 15.2 1.0
C28 A:7NL203 3.1 19.0 1.0
C29 A:7NL203 3.5 19.2 1.0
C30 A:7NL203 3.9 20.6 1.0
O A:HOH325 4.0 31.8 1.0
OD1 A:ASP92 4.0 20.8 1.0
NZ A:LYS88 4.2 28.2 1.0
C22 A:7NL203 4.5 18.5 1.0
CG A:ASP92 4.8 18.4 1.0
O11 A:7NL203 4.8 16.2 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 23:54:53 2025

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