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Fluorine in PDB 3vc4: Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design

Enzymatic activity of Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design

All present enzymatic activity of Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design:
2.7.11.1;

Protein crystallography data

The structure of Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design, PDB code: 3vc4 was solved by J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.30 / 2.23
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 98.496, 98.496, 81.025, 90.00, 90.00, 120.00
R / Rfree (%) 25.7 / 31.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design (pdb code 3vc4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design, PDB code: 3vc4:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3vc4

Go back to Fluorine Binding Sites List in 3vc4
Fluorine binding site 1 out of 3 in the Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:66.2
occ:1.00
F16 A:0FS1 0.0 66.2 1.0
C12 A:0FS1 1.3 62.7 1.0
F18 A:0FS1 2.2 66.7 1.0
F17 A:0FS1 2.3 60.3 1.0
C04 A:0FS1 2.3 58.8 1.0
C02 A:0FS1 2.8 57.7 1.0
CD1 A:LEU174 3.2 27.9 1.0
C06 A:0FS1 3.6 54.8 1.0
CG A:ARG122 3.7 37.2 1.0
CG1 A:VAL126 3.9 37.8 1.0
CD A:PRO123 4.0 41.8 1.0
C03 A:0FS1 4.1 55.3 1.0
CG2 A:VAL126 4.2 39.9 1.0
CB A:ARG122 4.3 38.7 1.0
CD A:ARG122 4.3 33.8 1.0
CA A:ARG122 4.4 39.7 1.0
CG A:PRO123 4.5 43.7 1.0
CG A:LEU174 4.5 33.1 1.0
CB A:VAL126 4.5 39.9 1.0
C05 A:0FS1 4.6 54.2 1.0
O A:PRO123 4.6 44.6 1.0
N A:PRO123 4.7 42.8 1.0
CD2 A:LEU174 4.7 25.3 1.0
C01 A:0FS1 4.9 55.4 1.0
C A:ARG122 5.0 41.0 1.0
O A:GLU121 5.0 40.3 1.0

Fluorine binding site 2 out of 3 in 3vc4

Go back to Fluorine Binding Sites List in 3vc4
Fluorine binding site 2 out of 3 in the Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:60.3
occ:1.00
F17 A:0FS1 0.0 60.3 1.0
C12 A:0FS1 1.4 62.7 1.0
F18 A:0FS1 2.2 66.7 1.0
F16 A:0FS1 2.3 66.2 1.0
C04 A:0FS1 2.3 58.8 1.0
C06 A:0FS1 2.7 54.8 1.0
O A:GLU121 3.4 40.3 1.0
CD1 A:LEU174 3.6 27.9 1.0
C02 A:0FS1 3.6 57.7 1.0
CB A:ALA65 3.7 33.0 1.0
CD1 A:ILE104 4.0 35.5 1.0
C05 A:0FS1 4.0 54.2 1.0
CB A:ARG122 4.0 38.7 1.0
CA A:ARG122 4.0 39.7 1.0
CG A:ARG122 4.2 37.2 1.0
CD A:PRO123 4.3 41.8 1.0
C A:GLU121 4.5 38.6 1.0
S10 A:0FS1 4.6 51.3 1.0
C03 A:0FS1 4.8 55.3 1.0
N A:ARG122 4.8 38.6 1.0
CD A:ARG122 4.9 33.8 1.0
C01 A:0FS1 4.9 55.4 1.0
C13 A:0FS1 5.0 50.0 1.0

Fluorine binding site 3 out of 3 in 3vc4

Go back to Fluorine Binding Sites List in 3vc4
Fluorine binding site 3 out of 3 in the Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Exploitation of Hydrogen Bonding Constraints and Flat Hydrophobic Energy Landscapes in Pim-1 Kinase Needle Screening and Inhibitor Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:66.7
occ:1.00
F18 A:0FS1 0.0 66.7 1.0
C12 A:0FS1 1.3 62.7 1.0
C04 A:0FS1 2.1 58.8 1.0
F16 A:0FS1 2.2 66.2 1.0
F17 A:0FS1 2.2 60.3 1.0
C02 A:0FS1 2.9 57.7 1.0
C06 A:0FS1 3.1 54.8 1.0
CD A:ARG122 3.2 33.8 1.0
CG A:ARG122 3.2 37.2 1.0
CB A:ALA65 3.4 33.0 1.0
CD1 A:LEU44 3.5 37.9 1.0
CB A:ARG122 3.7 38.7 1.0
C03 A:0FS1 4.1 55.3 1.0
C05 A:0FS1 4.2 54.2 1.0
CA A:ARG122 4.4 39.7 1.0
CA A:ALA65 4.4 34.8 1.0
NE A:ARG122 4.5 34.0 1.0
C01 A:0FS1 4.6 55.4 1.0
O A:GLU121 4.8 40.3 1.0
N A:ALA65 4.9 36.1 1.0
CD1 A:LEU174 5.0 27.9 1.0
CG A:LEU44 5.0 41.9 1.0

Reference:

A.C.Good, J.Liu, B.Hirth, G.Asmussen, Y.Xiang, H.P.Biemann, K.A.Bishop, T.Fremgen, M.Fitzgerald, T.Gladysheva, A.Jain, K.Jancsics, M.Metz, A.Papoulis, R.Skerlj, J.D.Stepp, R.R.Wei. Implications of Promiscuous Pim-1 Kinase Fragment Inhibitor Hydrophobic Interactions For Fragment-Based Drug Design. J.Med.Chem. V. 55 2641 2012.
ISSN: ISSN 0022-2623
PubMed: 22339127
DOI: 10.1021/JM2014698
Page generated: Mon Jul 14 19:51:39 2025

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