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Fluorine in PDB 3fmh: P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((R)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One

Enzymatic activity of P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((R)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One

All present enzymatic activity of P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((R)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One:
2.7.11.24;

Protein crystallography data

The structure of P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((R)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One, PDB code: 3fmh was solved by A.Kuglstatter, M.Ghate, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.66 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.654, 85.914, 126.370, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((R)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One (pdb code 3fmh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((R)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One, PDB code: 3fmh:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3fmh

Go back to Fluorine Binding Sites List in 3fmh
Fluorine binding site 1 out of 2 in the P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((R)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((R)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F361

b:37.1
occ:1.00
F23 A:533361 0.0 37.1 1.0
C19 A:533361 1.3 37.0 1.0
C18 A:533361 2.4 36.9 1.0
C20 A:533361 2.4 36.3 1.0
C A:VAL105 3.3 30.1 1.0
N A:VAL105 3.3 30.2 1.0
CB A:LEU104 3.3 30.9 1.0
O A:VAL105 3.4 29.9 1.0
C A:LEU104 3.4 30.7 1.0
CD1 A:LEU86 3.5 33.1 1.0
N A:THR106 3.5 30.5 1.0
CB A:THR106 3.6 31.0 1.0
C17 A:533361 3.6 36.9 1.0
C21 A:533361 3.6 36.8 1.0
CA A:VAL105 3.7 30.2 1.0
O A:LEU104 3.7 30.8 1.0
CA A:LEU104 3.9 31.0 1.0
CG2 A:THR106 4.1 30.7 1.0
CA A:THR106 4.1 30.8 1.0
C16 A:533361 4.1 37.2 1.0
CD1 A:LEU75 4.2 31.4 1.0
CG A:LEU104 4.5 30.5 1.0
OG1 A:THR106 4.7 30.0 1.0
O A:GLY85 4.7 34.8 1.0
F22 A:533361 4.7 36.5 1.0
O A:ALA51 4.8 33.4 1.0
CD1 A:LEU104 4.8 30.9 1.0
CG A:LEU86 4.9 33.3 1.0
CD2 A:LEU104 4.9 30.3 1.0
CD2 A:LEU75 4.9 31.6 1.0
CA A:LEU86 5.0 32.9 1.0

Fluorine binding site 2 out of 2 in 3fmh

Go back to Fluorine Binding Sites List in 3fmh
Fluorine binding site 2 out of 2 in the P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((R)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((R)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F361

b:36.5
occ:1.00
F22 A:533361 0.0 36.5 1.0
C21 A:533361 1.3 36.8 1.0
C20 A:533361 2.4 36.3 1.0
C16 A:533361 2.4 37.2 1.0
O15 A:533361 2.8 38.4 1.0
C12 A:533361 3.2 38.9 1.0
C13 A:533361 3.2 39.0 1.0
CG1 A:VAL38 3.4 41.5 1.0
CB A:LYS53 3.4 34.7 1.0
CB A:ALA51 3.6 33.5 1.0
C19 A:533361 3.6 37.0 1.0
C17 A:533361 3.6 36.9 1.0
O A:ALA51 3.7 33.4 1.0
CG2 A:VAL38 3.7 41.9 1.0
N A:LYS53 3.7 34.4 1.0
C A:ALA51 3.8 33.3 1.0
C A:VAL52 4.1 33.9 1.0
CA A:LYS53 4.1 34.9 1.0
C18 A:533361 4.1 36.9 1.0
CB A:VAL38 4.2 41.8 1.0
N A:VAL52 4.2 33.2 1.0
C11 A:533361 4.2 39.0 1.0
C8 A:533361 4.2 39.1 1.0
CG2 A:THR106 4.2 30.7 1.0
CA A:ALA51 4.3 33.5 1.0
O A:LEU104 4.5 30.8 1.0
CA A:VAL52 4.5 33.4 1.0
CD A:LYS53 4.5 34.8 1.0
CG A:LYS53 4.5 34.9 1.0
O A:VAL52 4.6 34.0 1.0
F23 A:533361 4.7 37.1 1.0
O14 A:533361 4.7 38.8 1.0
C6 A:533361 4.9 38.7 1.0
CA A:VAL38 5.0 41.6 1.0
CE A:LYS53 5.0 35.0 1.0

Reference:

M.Soth, A.Kuglstatter, D.Goldstein. The Discovery of Pamapimod and R1487 As Orally Bioavailable and Highly Selective Inhibitors of P38 Map Kinase To Be Published.
Page generated: Mon Jul 14 16:21:08 2025

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