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Fluorine in PDB 3k3j: P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121

Enzymatic activity of P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121

All present enzymatic activity of P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121:
2.7.11.24;

Protein crystallography data

The structure of P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121, PDB code: 3k3j was solved by S.L.Kazmirski, J.P.Dinitto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.51 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.179, 74.722, 77.733, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121 (pdb code 3k3j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121, PDB code: 3k3j:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3k3j

Go back to Fluorine Binding Sites List in 3k3j
Fluorine binding site 1 out of 6 in the P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F361

b:56.3
occ:1.00
 F4 A:F4C361 0.0 56.3 1.0
C14 A:F4C361 1.3 56.7 1.0
C15 A:F4C361 2.3 55.4 1.0
C16 A:F4C361 2.4 56.9 1.0
CD1 A:ILE141 3.2 37.7 1.0
CD2 A:HIS148 3.4 38.2 1.0
C13 A:F4C361 3.6 57.9 1.0
C12 A:F4C361 3.6 57.3 1.0
CG1 A:ILE141 3.9 36.7 1.0
C8 A:F4C361 4.1 58.3 1.0
CG2 A:ILE166 4.1 39.7 1.0
NE2 A:HIS148 4.3 40.3 1.0
CG1 A:VAL83 4.3 39.0 1.0
CG A:HIS148 4.4 36.6 1.0
CG2 A:ILE141 4.4 37.6 1.0
SD A:MET78 4.8 41.8 1.0
CB A:HIS148 4.8 38.0 1.0
CB A:ILE141 4.8 36.3 1.0

Fluorine binding site 2 out of 6 in 3k3j

Go back to Fluorine Binding Sites List in 3k3j
Fluorine binding site 2 out of 6 in the P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F361

b:65.2
occ:1.00
 F1 A:F4C361 0.0 65.2 1.0
C5 A:F4C361 1.3 65.3 1.0
F3 A:F4C361 2.2 68.9 1.0
F2 A:F4C361 2.2 67.9 1.0
C7 A:F4C361 2.3 62.6 1.0
C17 A:F4C361 2.6 60.4 1.0
CG1 A:VAL38 3.3 57.8 1.0
CB A:ALA51 3.5 49.7 1.0
C9 A:F4C361 3.6 61.3 1.0
CG2 A:VAL38 3.9 58.6 1.0
C23 A:F4C361 4.0 62.9 1.0
C11 A:F4C361 4.1 60.8 1.0
CB A:VAL38 4.2 59.4 1.0
OG1 A:THR106 4.4 48.3 1.0
CB A:LYS53 4.4 45.2 1.0
C A:ALA51 4.5 48.6 1.0
CA A:ALA51 4.6 50.0 1.0
CE1 A:PHE169 4.6 66.8 1.0
C22 A:F4C361 4.7 62.9 1.0
O A:ALA51 4.8 47.9 1.0
C24 A:F4C361 4.8 63.2 1.0
N A:LYS53 4.9 44.5 1.0
N A:VAL52 4.9 46.1 1.0
C A:VAL52 5.0 44.7 1.0

Fluorine binding site 3 out of 6 in 3k3j

Go back to Fluorine Binding Sites List in 3k3j
Fluorine binding site 3 out of 6 in the P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F361

b:67.9
occ:1.00
 F2 A:F4C361 0.0 67.9 1.0
C5 A:F4C361 1.3 65.3 1.0
F3 A:F4C361 2.2 68.9 1.0
F1 A:F4C361 2.2 65.2 1.0
C7 A:F4C361 2.3 62.6 1.0
C9 A:F4C361 3.0 61.3 1.0
C11 A:F4C361 3.1 60.8 1.0
C17 A:F4C361 3.3 60.4 1.0
CE1 A:PHE169 3.5 66.8 1.0
OG1 A:THR106 4.0 48.3 1.0
CZ A:PHE169 4.2 66.0 1.0
CD1 A:PHE169 4.2 65.6 1.0
C22 A:F4C361 4.3 62.9 1.0
N3 A:F4C361 4.4 58.0 1.0
CB A:ALA51 4.4 49.7 1.0
C23 A:F4C361 4.5 62.9 1.0
CD1 A:ILE84 4.5 51.2 1.0
CD1 A:LEU167 4.5 48.2 1.0
C24 A:F4C361 4.9 63.2 1.0

Fluorine binding site 4 out of 6 in 3k3j

Go back to Fluorine Binding Sites List in 3k3j
Fluorine binding site 4 out of 6 in the P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F361

b:68.9
occ:1.00
 F3 A:F4C361 0.0 68.9 1.0
C5 A:F4C361 1.3 65.3 1.0
F2 A:F4C361 2.2 67.9 1.0
F1 A:F4C361 2.2 65.2 1.0
C7 A:F4C361 2.3 62.6 1.0
C11 A:F4C361 2.6 60.8 1.0
C9 A:F4C361 2.8 61.3 1.0
CE1 A:PHE169 3.5 66.8 1.0
C17 A:F4C361 3.5 60.4 1.0
O A:HOH435 3.6 53.7 1.0
CD1 A:PHE169 3.6 65.6 1.0
N3 A:F4C361 4.0 58.0 1.0
CG2 A:VAL38 4.0 58.6 1.0
C22 A:F4C361 4.1 62.9 1.0
CD A:LYS53 4.3 49.4 1.0
O2 A:F4C361 4.5 60.4 1.0
C23 A:F4C361 4.6 62.9 1.0
CG1 A:VAL38 4.6 57.8 1.0
CB A:LYS53 4.7 45.2 1.0
CE A:LYS53 4.7 57.5 1.0
C6 A:F4C361 4.7 59.6 1.0
CZ A:PHE169 4.7 66.0 1.0
CG A:LYS53 4.8 47.5 1.0
C24 A:F4C361 4.8 63.2 1.0
CG A:PHE169 4.9 64.1 1.0
CB A:VAL38 5.0 59.4 1.0

Fluorine binding site 5 out of 6 in 3k3j

Go back to Fluorine Binding Sites List in 3k3j
Fluorine binding site 5 out of 6 in the P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F362

b:41.3
occ:1.00
 F18 A:I46362 0.0 41.3 1.0
C10 A:I46362 1.3 42.2 1.0
C3 A:I46362 2.3 40.8 1.0
C4 A:I46362 2.4 39.6 1.0
CD1 A:ILE259 2.6 58.9 1.0
CG1 A:ILE259 3.4 57.8 1.0
C1 A:I46362 3.6 38.7 1.0
C2 A:I46362 3.6 41.8 1.0
CG A:PRO242 3.9 44.4 1.0
CD1 A:LEU195 4.0 40.2 1.0
CD2 A:LEU232 4.0 44.1 1.0
C9 A:I46362 4.1 38.3 1.0
CD2 A:LEU195 4.1 43.6 1.0
CD1 A:LEU232 4.2 45.9 1.0
CD1 A:LEU236 4.2 42.4 1.0
CD A:PRO242 4.4 43.8 1.0
CG A:LEU195 4.5 45.3 1.0
CG A:LEU232 4.6 47.4 1.0
CD2 A:LEU236 4.6 42.7 1.0
CB A:ILE259 4.7 58.7 1.0
CG2 A:ILE259 4.9 55.6 1.0
CG A:LEU236 5.0 45.2 1.0

Fluorine binding site 6 out of 6 in 3k3j

Go back to Fluorine Binding Sites List in 3k3j
Fluorine binding site 6 out of 6 in the P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of P38ALPHA Bound to Novel Dfg-Out Compound Pf-00416121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F362

b:38.5
occ:1.00
 F19 A:I46362 0.0 38.5 1.0
C12 A:I46362 1.4 36.6 1.0
N16 A:I46362 2.3 35.0 1.0
C7 A:I46362 2.4 32.5 1.0
O A:HOH450 3.1 51.3 1.0
CD2 A:LEU195 3.4 43.6 1.0
CB A:TRP197 3.6 43.3 1.0
C6 A:I46362 3.6 32.8 1.0
CG A:TRP197 3.6 41.4 1.0
C11 A:I46362 3.6 31.8 1.0
CD1 A:TRP197 3.7 42.4 1.0
O A:HOH388 3.9 38.3 1.0
CG2 A:ILE250 4.0 43.8 1.0
C5 A:I46362 4.1 32.2 1.0
CA A:TRP197 4.2 45.5 1.0
CD2 A:TRP197 4.3 40.1 1.0
CG A:LEU195 4.4 45.3 1.0
CG1 A:ILE250 4.5 42.7 1.0
NE1 A:TRP197 4.5 40.2 1.0
CB A:ILE250 4.6 43.7 1.0
CA A:ILE250 4.7 43.7 1.0
N A:TRP197 4.8 45.6 1.0
CE2 A:TRP197 4.8 41.8 1.0
C14 A:I46362 4.9 31.9 1.0
CB A:LEU195 4.9 43.9 1.0

Reference:

H.Tecle, F.Feru, H.Liu, C.Kuhn, G.Rennie, M.Morris, J.Shao, A.C.Cheng, D.Gikunju, J.Miret, R.Coli, S.H.Xi, S.L.Clugston, S.Low, S.Kazmirski, Y.H.Ding, Q.Cao, T.L.Johnson, G.D.Deshmukh, J.P.Dinitto, J.C.Wu, J.M.English. The Design, Synthesis and Potential Utility of Fluorescence Probes That Target Dfg-Out Conformation of P38ALPHA For High Throughput Screening Binding Assay. Chem.Biol.Drug Des. V. 74 547 2009.
ISSN: ISSN 1747-0277
PubMed: 19843080
DOI: 10.1111/J.1747-0285.2009.00884.X
Page generated: Wed Jul 31 19:47:01 2024

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