Fluorine in PDB 7rt5: Crystal Structure of Kras G12D with Compound 36 (4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-7-(8-Ethynyl-7-Fluoronaphthalen-1-Yl)- 8-Fluoro-2-{[(4S,7AS)-Tetrahydro-1H-Pyrrolizin-7A(5H)- Yl]Methoxy}Pyrido[4,3-D]Pyrimidine) Bound

Enzymatic activity of Crystal Structure of Kras G12D with Compound 36 (4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-7-(8-Ethynyl-7-Fluoronaphthalen-1-Yl)- 8-Fluoro-2-{[(4S,7AS)-Tetrahydro-1H-Pyrrolizin-7A(5H)- Yl]Methoxy}Pyrido[4,3-D]Pyrimidine) Bound

All present enzymatic activity of Crystal Structure of Kras G12D with Compound 36 (4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-7-(8-Ethynyl-7-Fluoronaphthalen-1-Yl)- 8-Fluoro-2-{[(4S,7AS)-Tetrahydro-1H-Pyrrolizin-7A(5H)- Yl]Methoxy}Pyrido[4,3-D]Pyrimidine) Bound:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Kras G12D with Compound 36 (4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-7-(8-Ethynyl-7-Fluoronaphthalen-1-Yl)- 8-Fluoro-2-{[(4S,7AS)-Tetrahydro-1H-Pyrrolizin-7A(5H)- Yl]Methoxy}Pyrido[4,3-D]Pyrimidine) Bound, PDB code: 7rt5 was solved by R.J.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) 44.81 / 1.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.865, 51.935, 88.658, 90, 90, 90
R / Rfree (%) 16.3 / 18.7

Other elements in 7rt5:

The structure of Crystal Structure of Kras G12D with Compound 36 (4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-7-(8-Ethynyl-7-Fluoronaphthalen-1-Yl)- 8-Fluoro-2-{[(4S,7AS)-Tetrahydro-1H-Pyrrolizin-7A(5H)- Yl]Methoxy}Pyrido[4,3-D]Pyrimidine) 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 36 (4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-7-(8-Ethynyl-7-Fluoronaphthalen-1-Yl)- 8-Fluoro-2-{[(4S,7AS)-Tetrahydro-1H-Pyrrolizin-7A(5H)- Yl]Methoxy}Pyrido[4,3-D]Pyrimidine) Bound (pdb code 7rt5). 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 36 (4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-7-(8-Ethynyl-7-Fluoronaphthalen-1-Yl)- 8-Fluoro-2-{[(4S,7AS)-Tetrahydro-1H-Pyrrolizin-7A(5H)- Yl]Methoxy}Pyrido[4,3-D]Pyrimidine) Bound, PDB code: 7rt5:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7rt5

Go back to Fluorine Binding Sites List in 7rt5
Fluorine binding site 1 out of 2 in the Crystal Structure of Kras G12D with Compound 36 (4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-7-(8-Ethynyl-7-Fluoronaphthalen-1-Yl)- 8-Fluoro-2-{[(4S,7AS)-Tetrahydro-1H-Pyrrolizin-7A(5H)- Yl]Methoxy}Pyrido[4,3-D]Pyrimidine) 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 36 (4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-7-(8-Ethynyl-7-Fluoronaphthalen-1-Yl)- 8-Fluoro-2-{[(4S,7AS)-Tetrahydro-1H-Pyrrolizin-7A(5H)- Yl]Methoxy}Pyrido[4,3-D]Pyrimidine) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:13.1
occ:1.00
 F01 A:7OE202 0.0 13.1 1.0
C07 A:7OE202 1.4 12.7 1.0
C02 A:7OE202 2.3 13.4 1.0
C06 A:7OE202 2.4 12.7 1.0
N01 A:7OE202 2.7 12.4 1.0
C08 A:7OE202 2.8 14.2 1.0
C20 A:7OE202 3.2 11.6 1.0
NE2 A:HIS95 3.2 14.1 1.0
CG A:GLN99 3.4 13.0 1.0
C24 A:7OE202 3.4 11.6 1.0
OH A:TYR64 3.4 17.4 1.0
C32 A:7OE202 3.5 12.4 1.0
CE2 A:TYR64 3.5 16.8 1.0
C16 A:7OE202 3.6 14.3 1.0
N03 A:7OE202 3.6 12.3 1.0
C01 A:7OE202 3.6 13.2 1.0
CZ A:TYR64 3.9 16.8 1.0
CB A:GLN99 3.9 12.6 1.0
C33 A:7OE202 3.9 12.6 1.0
CD2 A:HIS95 4.0 12.9 1.0
CE1 A:HIS95 4.0 14.2 1.0
C03 A:7OE202 4.0 11.7 1.0
C05 A:7OE202 4.1 13.8 1.0
C19 A:7OE202 4.1 12.5 1.0
CD A:GLN99 4.3 15.5 1.0
C23 A:7OE202 4.4 12.2 1.0
CE1 A:TYR96 4.4 11.2 1.0
C17 A:7OE202 4.5 15.1 1.0
CD1 A:TYR96 4.5 11.0 1.0
OE1 A:GLN99 4.6 15.8 1.0
CD2 A:TYR64 4.6 19.8 1.0
C18 A:7OE202 4.7 13.9 1.0
C04 A:7OE202 4.8 11.7 1.0
O01 A:7OE202 4.8 11.5 1.0
N02 A:7OE202 5.0 11.9 1.0

Fluorine binding site 2 out of 2 in 7rt5

Go back to Fluorine Binding Sites List in 7rt5
Fluorine binding site 2 out of 2 in the Crystal Structure of Kras G12D with Compound 36 (4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-7-(8-Ethynyl-7-Fluoronaphthalen-1-Yl)- 8-Fluoro-2-{[(4S,7AS)-Tetrahydro-1H-Pyrrolizin-7A(5H)- Yl]Methoxy}Pyrido[4,3-D]Pyrimidine) 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 36 (4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-7-(8-Ethynyl-7-Fluoronaphthalen-1-Yl)- 8-Fluoro-2-{[(4S,7AS)-Tetrahydro-1H-Pyrrolizin-7A(5H)- Yl]Methoxy}Pyrido[4,3-D]Pyrimidine) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:13.5
occ:1.00
 F23 A:7OE202 0.0 13.5 1.0
C23 A:7OE202 1.4 12.2 1.0
C22 A:7OE202 2.4 13.3 1.0
C24 A:7OE202 2.4 11.6 1.0
C32 A:7OE202 2.7 12.4 1.0
C33 A:7OE202 3.4 12.6 1.0
CG1 A:VAL9 3.4 11.0 1.0
CG1 A:ILE100 3.5 12.1 1.0
C21 A:7OE202 3.6 13.4 1.0
C20 A:7OE202 3.6 11.6 1.0
CD1 A:ILE100 4.0 12.9 1.0
CB A:VAL9 4.0 9.0 1.0
C19 A:7OE202 4.1 12.5 1.0
CG2 A:VAL9 4.2 10.6 1.0
O A:TYR96 4.2 11.9 1.0
CD2 A:PHE78 4.4 11.8 1.0
CE2 A:PHE78 4.4 13.1 1.0
SD A:MET72 4.5 21.6 1.0
CD1 A:TYR96 4.5 11.0 1.0
N A:ILE100 4.6 12.2 1.0
CB A:GLN99 4.7 12.6 1.0
CB A:ILE100 4.8 11.5 1.0
C08 A:7OE202 4.8 14.2 1.0
CE A:MET72 4.9 23.2 1.0
CB A:TYR96 4.9 10.7 1.0
CA A:ILE100 4.9 13.2 1.0
C A:TYR96 5.0 11.8 1.0
CA A:TYR96 5.0 10.9 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: Fri Aug 2 12:33:14 2024

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