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Fluorine in PDB 3hp5: Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound

Enzymatic activity of Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound

All present enzymatic activity of Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound:
2.7.11.24;

Protein crystallography data

The structure of Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound, PDB code: 3hp5 was solved by H.-S.Shieh, J.M.Williams, R.A.Stegeman, R.G.Kurumbail, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.01 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.045, 74.022, 76.697, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.2

Other elements in 3hp5:

The structure of Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound (pdb code 3hp5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound, PDB code: 3hp5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3hp5

Go back to Fluorine Binding Sites List in 3hp5
Fluorine binding site 1 out of 6 in the Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound


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 Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.1
occ:1.00
 F1 A:52P401 0.0 34.1 1.0
C2 A:52P401 1.3 34.1 1.0
C3 A:52P401 2.3 33.7 1.0
C28 A:52P401 2.4 34.8 1.0
C A:VAL105 3.4 41.5 1.0
CB A:LEU104 3.4 40.9 1.0
C A:LEU104 3.4 41.2 1.0
N A:VAL105 3.5 41.2 1.0
O A:VAL105 3.5 41.1 1.0
CD2 A:LEU86 3.5 41.2 1.0
CB A:THR106 3.6 42.0 1.0
C4 A:52P401 3.6 35.2 1.0
O A:LEU104 3.6 41.0 1.0
C26 A:52P401 3.6 35.7 1.0
N A:THR106 3.7 41.8 1.0
CA A:VAL105 3.7 41.6 1.0
CG2 A:THR106 3.9 41.0 1.0
CA A:LEU104 4.0 41.0 1.0
C5 A:52P401 4.1 35.2 1.0
CA A:THR106 4.2 42.1 1.0
CD1 A:LEU75 4.4 41.8 1.0
O A:GLY85 4.4 41.2 1.0
O A:ALA51 4.6 38.7 1.0
OG1 A:THR106 4.6 42.2 1.0
CG A:LEU104 4.7 40.4 1.0
F27 A:52P401 4.7 34.6 1.0
CG2 A:ILE84 4.8 42.0 1.0
CD1 A:LEU104 4.9 38.8 1.0
CG A:LEU86 4.9 42.2 1.0
CD2 A:LEU75 4.9 41.1 1.0

Fluorine binding site 2 out of 6 in 3hp5

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Fluorine binding site 2 out of 6 in the Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound


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 Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.6
occ:1.00
 F27 A:52P401 0.0 34.6 1.0
C26 A:52P401 1.3 35.7 1.0
C5 A:52P401 2.3 35.2 1.0
C28 A:52P401 2.4 34.8 1.0
S6 A:52P401 3.0 36.6 1.0
N25 A:52P401 3.2 38.1 1.0
C7 A:52P401 3.2 37.9 1.0
CB A:ALA51 3.4 38.8 1.0
C A:ALA51 3.4 39.4 1.0
O A:ALA51 3.5 38.7 1.0
N A:LYS53 3.5 40.7 1.0
C4 A:52P401 3.6 35.2 1.0
C A:VAL52 3.6 40.5 1.0
C2 A:52P401 3.6 34.1 1.0
N A:VAL52 3.6 39.8 1.0
CG1 A:VAL38 3.6 38.8 1.0
CB A:LYS53 3.7 41.0 1.0
CA A:VAL52 4.0 40.1 1.0
CA A:ALA51 4.0 39.5 1.0
CA A:LYS53 4.0 41.1 1.0
C3 A:52P401 4.1 33.7 1.0
O A:VAL52 4.1 40.2 1.0
N24 A:52P401 4.2 38.3 1.0
C8 A:52P401 4.2 38.3 1.0
CG2 A:VAL38 4.4 40.4 1.0
O A:LEU104 4.4 41.0 1.0
CG2 A:THR106 4.5 41.0 1.0
CB A:VAL38 4.6 40.4 1.0
CG A:LYS53 4.6 41.2 1.0
F1 A:52P401 4.7 34.1 1.0
C23 A:52P401 4.7 38.1 1.0
C9 A:52P401 5.0 38.4 1.0
C10 A:52P401 5.0 38.8 1.0

Fluorine binding site 3 out of 6 in 3hp5

Go back to Fluorine Binding Sites List in 3hp5
Fluorine binding site 3 out of 6 in the Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:37.1
occ:1.00
 F18 A:I46402 0.0 37.1 1.0
C10 A:I46402 1.3 35.4 1.0
C3 A:I46402 2.3 35.9 1.0
C4 A:I46402 2.3 34.2 1.0
CD1 A:ILE259 3.3 44.5 1.0
CG1 A:ILE259 3.5 44.7 1.0
C2 A:I46402 3.6 33.9 1.0
C1 A:I46402 3.6 32.7 1.0
CG2 A:ILE259 3.9 44.4 1.0
CG A:PRO242 3.9 40.0 1.0
C9 A:I46402 4.1 33.3 1.0
CD2 A:LEU232 4.1 40.4 1.0
CD1 A:LEU195 4.1 46.1 1.0
CD1 A:LEU232 4.2 40.0 1.0
CG A:LEU195 4.2 47.1 1.0
CB A:ILE259 4.3 44.3 1.0
CD A:PRO242 4.4 40.5 1.0
CD1 A:LEU236 4.4 42.4 1.0
CD2 A:LEU236 4.4 40.4 1.0
CD2 A:LEU195 4.6 44.7 1.0
CG A:LEU232 4.7 41.3 1.0
CG A:LEU236 4.8 40.8 1.0

Fluorine binding site 4 out of 6 in 3hp5

Go back to Fluorine Binding Sites List in 3hp5
Fluorine binding site 4 out of 6 in the Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:35.1
occ:1.00
 F19 A:I46402 0.0 35.1 1.0
C12 A:I46402 1.3 32.3 1.0
N16 A:I46402 2.3 30.6 1.0
C7 A:I46402 2.3 31.1 1.0
O A:HOH590 3.3 42.1 1.0
C6 A:I46402 3.5 30.8 1.0
C11 A:I46402 3.6 32.2 1.0
CB A:TRP197 3.7 45.6 1.0
CG A:TRP197 3.7 45.2 1.0
CD1 A:LEU195 3.7 46.1 1.0
CD1 A:TRP197 3.8 44.5 1.0
CG2 A:ILE250 3.8 38.8 1.0
C5 A:I46402 4.0 31.0 1.0
O A:HOH558 4.0 23.9 1.0
CG1 A:ILE250 4.3 39.4 1.0
CD2 A:TRP197 4.3 44.1 1.0
CB A:ILE250 4.5 39.3 1.0
CA A:TRP197 4.5 46.5 1.0
CA A:ILE250 4.5 39.6 1.0
NE1 A:TRP197 4.5 44.0 1.0
CB A:LEU195 4.7 47.0 1.0
C14 A:I46402 4.8 31.9 1.0
CE2 A:TRP197 4.8 44.1 1.0
CG A:LEU195 4.9 47.1 1.0
N A:TRP197 4.9 46.0 1.0

Fluorine binding site 5 out of 6 in 3hp5

Go back to Fluorine Binding Sites List in 3hp5
Fluorine binding site 5 out of 6 in the Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:61.1
occ:1.00
 F18 A:I46403 0.0 61.1 1.0
C10 A:I46403 1.3 61.0 1.0
C3 A:I46403 2.3 60.4 1.0
C4 A:I46403 2.3 60.4 1.0
C2 A:I46403 3.6 61.2 1.0
C1 A:I46403 3.6 60.5 1.0
C9 A:I46403 4.1 61.1 1.0
O A:THR44 4.2 40.0 1.0

Fluorine binding site 6 out of 6 in 3hp5

Go back to Fluorine Binding Sites List in 3hp5
Fluorine binding site 6 out of 6 in the Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human P38ALPHA Complexed with A Pyrimidopyridazinone Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:63.7
occ:1.00
 F19 A:I46403 0.0 63.7 1.0
C12 A:I46403 1.3 64.0 1.0
N16 A:I46403 2.3 64.5 1.0
C7 A:I46403 2.3 63.3 1.0
O A:HOH624 2.8 65.8 1.0
OE2 A:GLU22 3.0 46.4 1.0
C6 A:I46403 3.5 63.8 1.0
CD A:GLU22 3.6 44.4 1.0
C11 A:I46403 3.6 62.6 1.0
OG1 A:THR44 3.9 39.7 1.0
CG A:GLU22 3.9 44.5 1.0
C5 A:I46403 4.0 63.2 1.0
O A:GLU22 4.1 42.3 1.0
CA A:ARG23 4.2 42.8 1.0
C A:GLU22 4.3 42.9 1.0
N A:ARG23 4.4 42.8 1.0
OE1 A:GLU22 4.4 46.7 1.0
C2 A:I46403 4.5 61.2 1.0
CB A:GLU22 4.5 43.4 1.0
O A:HOH653 4.7 49.4 1.0
C14 A:I46403 4.8 61.4 1.0
CB A:THR44 4.8 39.6 1.0
C4 A:I46403 4.9 60.4 1.0
CB A:ARG23 4.9 42.9 1.0

Reference:

S.R.Selness, R.V.Devraj, J.B.Monahan, T.L.Boehm, J.K.Walker, B.Devadas, R.C.Durley, R.Kurumbail, H.Shieh, L.Xing, M.Hepperle, P.V.Rucker, K.D.Jerome, A.G.Benson, L.D.Marrufo, H.M.Madsen, J.Hitchcock, T.J.Owen, L.Christie, M.A.Promo, B.S.Hickory, E.Alvira, W.Naing, R.Blevis-Bal. Discovery of N-Substituted Pyridinones As Potent and Selective Inhibitors of P38 Kinase. Bioorg.Med.Chem.Lett. V. 19 5851 2009.
ISSN: ISSN 0960-894X
PubMed: 19751974
DOI: 10.1016/J.BMCL.2009.08.082
Page generated: Mon Jul 14 16:54:50 2025

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