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Fluorine in PDB 7rt3: Crystal Structure of Kras G12D with Compound 24 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S,4S,7AR)-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 24 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S,4S,7AR)-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 24 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S,4S,7AR)-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 24 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S,4S,7AR)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound, PDB code: 7rt3 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) 32.13 / 1.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.29, 53.257, 88.889, 90, 90, 90
R / Rfree (%) 16.4 / 19.9

Other elements in 7rt3:

The structure of Crystal Structure of Kras G12D with Compound 24 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S,4S,7AR)-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 24 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S,4S,7AR)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound (pdb code 7rt3). 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 24 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S,4S,7AR)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound, PDB code: 7rt3:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7rt3

Go back to Fluorine Binding Sites List in 7rt3
Fluorine binding site 1 out of 2 in the Crystal Structure of Kras G12D with Compound 24 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S,4S,7AR)-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 24 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S,4S,7AR)-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:F202

b:17.6
occ:1.00
 F01 A:7NZ202 0.0 17.6 1.0
C01 A:7NZ202 1.4 16.6 1.0
C02 A:7NZ202 2.3 15.6 1.0
C28 A:7NZ202 2.4 17.5 1.0
O A:HOH408 2.7 42.8 1.0
NZ A:LYS88 3.0 22.5 1.0
N06 A:7NZ202 3.0 14.0 1.0
C03 A:7NZ202 3.0 13.9 1.0
C29 A:7NZ202 3.2 15.8 1.0
C31 A:7NZ202 3.2 12.2 1.0
C30 A:7NZ202 3.8 13.6 1.0
OD1 A:ASP92 4.1 16.8 1.0
O A:HOH415 4.1 38.3 1.0
CE A:LYS88 4.2 34.3 1.0
C04 A:7NZ202 4.4 12.4 1.0
OD2 A:ASP92 4.6 19.9 1.0
CG A:ASP92 4.7 16.7 1.0
O A:HOH322 4.8 36.0 1.0

Fluorine binding site 2 out of 2 in 7rt3

Go back to Fluorine Binding Sites List in 7rt3
Fluorine binding site 2 out of 2 in the Crystal Structure of Kras G12D with Compound 24 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S,4S,7AR)-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 24 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2S,4S,7AR)-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:F202

b:13.8
occ:1.00
 F02 A:7NZ202 0.0 13.8 1.0
C15 A:7NZ202 1.4 12.0 1.0
C16 A:7NZ202 2.4 12.9 1.0
C14 A:7NZ202 2.4 12.3 1.0
N05 A:7NZ202 2.8 11.1 1.0
C17 A:7NZ202 2.8 14.5 1.0
C26 A:7NZ202 3.1 11.0 1.0
C18 A:7NZ202 3.1 13.0 1.0
NE2 A:HIS95 3.2 14.2 1.0
CE2 A:TYR64 3.3 17.1 1.0
OH A:TYR64 3.4 15.4 1.0
CG A:GLN99 3.4 13.5 1.0
N04 A:7NZ202 3.6 14.1 1.0
C13 A:7NZ202 3.6 11.5 1.0
CZ A:TYR64 3.7 15.3 1.0
C22 A:7NZ202 3.8 14.1 1.0
CD2 A:HIS95 3.9 15.5 1.0
C27 A:7NZ202 4.0 14.1 1.0
CB A:GLN99 4.0 13.0 1.0
CE1 A:HIS95 4.0 15.2 1.0
C05 A:7NZ202 4.1 12.7 1.0
C25 A:7NZ202 4.2 11.7 1.0
C19 A:7NZ202 4.2 14.8 1.0
CD2 A:TYR64 4.3 18.3 1.0
CD A:GLN99 4.4 13.7 1.0
CE1 A:TYR96 4.4 11.8 1.0
CD1 A:TYR96 4.5 13.3 1.0
OE1 A:GLN99 4.6 15.7 1.0
C21 A:7NZ202 4.7 18.1 1.0
C06 A:7NZ202 4.7 12.7 1.0
O01 A:7NZ202 4.8 12.8 1.0
C20 A:7NZ202 4.9 19.1 1.0
O A:HOH476 4.9 21.1 1.0
N01 A:7NZ202 4.9 12.1 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 23:55:23 2025

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