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Fluorine in PDB 4k1b: Structure of Pim-1 Kinase Bound to N-(5-(2-Fluorophenyl)-1H-Pyrrolo[2, 3-B]Pyridin-3-Yl)-5-((((3R,4R)-3-Fluoropiperidin-4-Yl)Methyl)Amino) Pyrazolo[1,5-A]Pyrimidine-3-Carboxamide

Enzymatic activity of Structure of Pim-1 Kinase Bound to N-(5-(2-Fluorophenyl)-1H-Pyrrolo[2, 3-B]Pyridin-3-Yl)-5-((((3R,4R)-3-Fluoropiperidin-4-Yl)Methyl)Amino) Pyrazolo[1,5-A]Pyrimidine-3-Carboxamide

All present enzymatic activity of Structure of Pim-1 Kinase Bound to N-(5-(2-Fluorophenyl)-1H-Pyrrolo[2, 3-B]Pyridin-3-Yl)-5-((((3R,4R)-3-Fluoropiperidin-4-Yl)Methyl)Amino) Pyrazolo[1,5-A]Pyrimidine-3-Carboxamide:
2.7.11.1;

Protein crystallography data

The structure of Structure of Pim-1 Kinase Bound to N-(5-(2-Fluorophenyl)-1H-Pyrrolo[2, 3-B]Pyridin-3-Yl)-5-((((3R,4R)-3-Fluoropiperidin-4-Yl)Methyl)Amino) Pyrazolo[1,5-A]Pyrimidine-3-Carboxamide, PDB code: 4k1b was solved by J.M.Murray, H.Wallweber, M.Steffek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 2.08
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 97.993, 97.993, 80.542, 90.00, 90.00, 120.00
R / Rfree (%) 17.1 / 19.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Pim-1 Kinase Bound to N-(5-(2-Fluorophenyl)-1H-Pyrrolo[2, 3-B]Pyridin-3-Yl)-5-((((3R,4R)-3-Fluoropiperidin-4-Yl)Methyl)Amino) Pyrazolo[1,5-A]Pyrimidine-3-Carboxamide (pdb code 4k1b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Pim-1 Kinase Bound to N-(5-(2-Fluorophenyl)-1H-Pyrrolo[2, 3-B]Pyridin-3-Yl)-5-((((3R,4R)-3-Fluoropiperidin-4-Yl)Methyl)Amino) Pyrazolo[1,5-A]Pyrimidine-3-Carboxamide, PDB code: 4k1b:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4k1b

Go back to Fluorine Binding Sites List in 4k1b
Fluorine binding site 1 out of 2 in the Structure of Pim-1 Kinase Bound to N-(5-(2-Fluorophenyl)-1H-Pyrrolo[2, 3-B]Pyridin-3-Yl)-5-((((3R,4R)-3-Fluoropiperidin-4-Yl)Methyl)Amino) Pyrazolo[1,5-A]Pyrimidine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Pim-1 Kinase Bound to N-(5-(2-Fluorophenyl)-1H-Pyrrolo[2, 3-B]Pyridin-3-Yl)-5-((((3R,4R)-3-Fluoropiperidin-4-Yl)Methyl)Amino) Pyrazolo[1,5-A]Pyrimidine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:85.0
occ:1.00
 F37 A:1OC402 0.0 85.0 1.0
C36 A:1OC402 1.4 76.3 1.0
C31 A:1OC402 2.4 71.5 1.0
C35 A:1OC402 2.4 71.8 1.0
C30 A:1OC402 2.9 66.8 1.0
CD1 A:ILE185 3.1 27.4 1.0
N29 A:1OC402 3.3 63.3 1.0
C26 A:1OC402 3.4 58.5 1.0
O A:GLU171 3.4 28.2 1.0
N25 A:1OC402 3.5 49.5 1.0
N34 A:1OC402 3.7 70.7 1.0
C32 A:1OC402 3.7 67.5 1.0
C27 A:1OC402 4.1 57.6 1.0
C33 A:1OC402 4.1 68.7 1.0
C24 A:1OC402 4.3 48.6 1.0
CG1 A:ILE185 4.4 25.7 1.0
C A:GLU171 4.6 29.8 1.0
OD1 A:ASN172 4.6 26.0 1.0
C28 A:1OC402 4.8 55.6 1.0
N23 A:1OC402 4.8 51.2 1.0
O A:HOH592 4.9 48.9 1.0
N17 A:1OC402 5.0 36.6 1.0

Fluorine binding site 2 out of 2 in 4k1b

Go back to Fluorine Binding Sites List in 4k1b
Fluorine binding site 2 out of 2 in the Structure of Pim-1 Kinase Bound to N-(5-(2-Fluorophenyl)-1H-Pyrrolo[2, 3-B]Pyridin-3-Yl)-5-((((3R,4R)-3-Fluoropiperidin-4-Yl)Methyl)Amino) Pyrazolo[1,5-A]Pyrimidine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Pim-1 Kinase Bound to N-(5-(2-Fluorophenyl)-1H-Pyrrolo[2, 3-B]Pyridin-3-Yl)-5-((((3R,4R)-3-Fluoropiperidin-4-Yl)Methyl)Amino) Pyrazolo[1,5-A]Pyrimidine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:87.2
occ:1.00
 F38 A:1OC402 0.0 87.2 1.0
C4 A:1OC402 1.4 79.0 1.0
C3 A:1OC402 2.3 77.4 1.0
C5 A:1OC402 2.4 67.8 1.0
C16 A:1OC402 2.8 50.4 1.0
C7 A:1OC402 2.9 52.5 1.0
CD1 A:LEU44 3.4 58.9 1.0
CG1 A:VAL126 3.6 43.3 1.0
C2 A:1OC402 3.6 74.5 1.0
C6 A:1OC402 3.7 71.8 1.0
CD2 A:LEU44 3.7 58.1 1.0
N15 A:1OC402 4.0 47.4 1.0
O A:HOH519 4.0 43.3 1.0
CG A:LEU44 4.1 57.2 1.0
C1 A:1OC402 4.1 74.9 1.0
CD A:ARG122 4.1 40.3 1.0
C8 A:1OC402 4.2 44.3 1.0
CG A:ARG122 4.6 37.4 1.0
CB A:LEU44 4.8 53.1 1.0
C14 A:1OC402 5.0 44.2 1.0

Reference:

X.Wang, S.Magnuson, R.Pastor, E.Fan, H.Hu, V.Tsui, W.Deng, J.Murray, M.Steffek, H.Wallweber, J.Moffat, J.Drummond, G.Chan, E.Harstad, A.J.Ebens. Discovery of Novel Pyrazolo[1,5-A]Pyrimidines As Potent Pan-Pim Inhibitors By Structure- and Property-Based Drug Design. Bioorg.Med.Chem.Lett. V. 23 3149 2013.
ISSN: ISSN 0960-894X
PubMed: 23623490
DOI: 10.1016/J.BMCL.2013.04.020
Page generated: Mon Jul 14 22:46:53 2025

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