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Fluorine in PDB 3fmk: P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((S)-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-((S)-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-((S)-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-((S)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One, PDB code: 3fmk 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) 43.27 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.483, 86.513, 124.307, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 22.4

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-((S)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One (pdb code 3fmk). 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-((S)-1-Methyl-2-Tetrazol-2-Yl-Ethylamino)-8H-Pyrido[2,3- D]Pyrimidin-7-One, PDB code: 3fmk:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3fmk

Go back to Fluorine Binding Sites List in 3fmk
Fluorine binding site 1 out of 2 in the P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((S)-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-((S)-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:20.8
occ:1.00
F23 A:FMK361 0.0 20.8 1.0
C19 A:FMK361 1.3 20.0 1.0
C18 A:FMK361 2.4 19.9 1.0
C20 A:FMK361 2.4 19.4 1.0
N A:VAL105 3.2 17.1 1.0
CB A:LEU104 3.3 17.7 1.0
C A:VAL105 3.3 17.0 1.0
C A:LEU104 3.3 17.4 1.0
O A:VAL105 3.4 16.7 1.0
CD1 A:LEU86 3.5 20.3 1.0
N A:THR106 3.6 17.0 1.0
O A:LEU104 3.6 17.3 1.0
C17 A:FMK361 3.6 20.2 1.0
CB A:THR106 3.6 17.3 1.0
C21 A:FMK361 3.6 19.6 1.0
CA A:VAL105 3.7 16.9 1.0
CA A:LEU104 3.8 17.6 1.0
CG2 A:THR106 4.0 17.5 1.0
CD1 A:LEU75 4.1 18.5 1.0
C16 A:FMK361 4.1 20.0 1.0
CA A:THR106 4.2 17.3 1.0
O A:GLY85 4.4 20.5 1.0
CG A:LEU104 4.5 17.1 1.0
OG1 A:THR106 4.7 16.8 1.0
F22 A:FMK361 4.7 20.5 1.0
O A:ALA51 4.8 18.6 1.0
CD1 A:LEU104 4.8 17.7 1.0
CD2 A:LEU75 4.9 17.9 1.0
CG A:LEU86 4.9 20.2 1.0
CA A:LEU86 5.0 19.8 1.0

Fluorine binding site 2 out of 2 in 3fmk

Go back to Fluorine Binding Sites List in 3fmk
Fluorine binding site 2 out of 2 in the P38 Kinase Crystal Structure in Complex with 6-(2,4-Difluoro-Phenoxy)- 8-Methyl-2-((S)-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-((S)-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:20.5
occ:1.00
F22 A:FMK361 0.0 20.5 1.0
C21 A:FMK361 1.3 19.6 1.0
C20 A:FMK361 2.4 19.4 1.0
C16 A:FMK361 2.4 20.0 1.0
O15 A:FMK361 2.8 20.8 1.0
C12 A:FMK361 3.0 20.7 1.0
C13 A:FMK361 3.1 20.9 1.0
CB A:LYS53 3.4 19.8 1.0
CG1 A:VAL38 3.5 23.2 1.0
C19 A:FMK361 3.6 20.0 1.0
C17 A:FMK361 3.6 20.2 1.0
CG2 A:VAL38 3.7 23.5 1.0
CB A:ALA51 3.7 18.6 1.0
N A:LYS53 3.8 19.3 1.0
O A:ALA51 3.8 18.6 1.0
C11 A:FMK361 3.8 21.1 1.0
C A:ALA51 3.9 18.6 1.0
CA A:LYS53 4.1 19.8 1.0
C8 A:FMK361 4.1 20.6 1.0
C A:VAL52 4.1 19.0 1.0
C18 A:FMK361 4.1 19.9 1.0
CB A:VAL38 4.2 23.5 1.0
N A:VAL52 4.3 18.7 1.0
O14 A:FMK361 4.4 21.2 1.0
CG2 A:THR106 4.4 17.5 1.0
CG A:LYS53 4.5 19.7 1.0
CA A:ALA51 4.5 18.6 1.0
CD A:LYS53 4.5 19.7 1.0
O A:LEU104 4.5 17.3 1.0
O A:VAL52 4.6 18.8 1.0
CA A:VAL52 4.6 18.8 1.0
N10 A:FMK361 4.7 21.2 1.0
F23 A:FMK361 4.7 20.8 1.0
C9 A:FMK361 4.8 21.0 1.0
CE A:LYS53 4.8 19.3 1.0
C6 A:FMK361 4.9 21.1 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: Sun Dec 13 11:46:15 2020

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