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Fluorine in PDB 6p5v: Structure of DCN1 Bound to N-((4S,5S)-7-Ethyl-4-(4-Fluorophenyl)-3- Methyl-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4-B]Pyridin-5- Yl)-3-Methylbenzamide

Enzymatic activity of Structure of DCN1 Bound to N-((4S,5S)-7-Ethyl-4-(4-Fluorophenyl)-3- Methyl-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4-B]Pyridin-5- Yl)-3-Methylbenzamide

All present enzymatic activity of Structure of DCN1 Bound to N-((4S,5S)-7-Ethyl-4-(4-Fluorophenyl)-3- Methyl-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4-B]Pyridin-5- Yl)-3-Methylbenzamide:
3.2.1.17;

Protein crystallography data

The structure of Structure of DCN1 Bound to N-((4S,5S)-7-Ethyl-4-(4-Fluorophenyl)-3- Methyl-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4-B]Pyridin-5- Yl)-3-Methylbenzamide, PDB code: 6p5v was solved by R.K.Guy, H.S.Kim, J.T.Hammill, D.C.Scott, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.13 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.310, 96.985, 60.072, 90.00, 106.09, 90.00
R / Rfree (%) 17.1 / 20.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of DCN1 Bound to N-((4S,5S)-7-Ethyl-4-(4-Fluorophenyl)-3- Methyl-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4-B]Pyridin-5- Yl)-3-Methylbenzamide (pdb code 6p5v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Structure of DCN1 Bound to N-((4S,5S)-7-Ethyl-4-(4-Fluorophenyl)-3- Methyl-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4-B]Pyridin-5- Yl)-3-Methylbenzamide, PDB code: 6p5v:

Fluorine binding site 1 out of 1 in 6p5v

Go back to Fluorine Binding Sites List in 6p5v
Fluorine binding site 1 out of 1 in the Structure of DCN1 Bound to N-((4S,5S)-7-Ethyl-4-(4-Fluorophenyl)-3- Methyl-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4-B]Pyridin-5- Yl)-3-Methylbenzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of DCN1 Bound to N-((4S,5S)-7-Ethyl-4-(4-Fluorophenyl)-3- Methyl-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4-B]Pyridin-5- Yl)-3-Methylbenzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1302

b:24.6
occ:1.00
 FAV A:O371302 0.0 24.6 1.0
CZ A:O371302 1.3 21.2 1.0
CE2 A:O371302 2.4 21.2 1.0
CE1 A:O371302 2.4 21.1 1.0
HB3 A:PRO1097 2.6 39.8 1.0
HE2 A:O371302 2.6 25.4 1.0
HE1 A:O371302 2.6 25.3 1.0
HA A:GLN1087 2.8 31.2 1.0
HG22 A:ILE1086 2.9 28.1 1.0
CA A:GLN1087 3.5 26.1 1.0
CB A:PRO1097 3.5 33.2 1.0
HB2 A:GLN1087 3.5 36.5 1.0
CD2 A:O371302 3.6 20.6 1.0
CD1 A:O371302 3.6 21.2 1.0
N A:GLN1087 3.7 25.2 1.0
HG A:CYS1090 3.7 34.7 1.0
SG A:CYS1090 3.8 29.0 1.0
CG2 A:ILE1086 3.8 23.4 1.0
C A:ILE1086 3.8 23.6 1.0
HB2 A:PRO1097 3.9 39.8 1.0
O A:ILE1086 3.9 23.1 1.0
HB2 A:CYS1090 3.9 31.1 1.0
CB A:GLN1087 4.0 30.4 1.0
H A:GLN1087 4.0 30.2 1.0
HG21 A:ILE1086 4.0 28.1 1.0
HB A:ILE1086 4.0 27.9 1.0
HG3 A:PRO1097 4.1 42.3 1.0
CG A:O371302 4.1 20.8 1.0
HA A:PRO1097 4.2 38.1 1.0
HG3 A:GLN1087 4.3 43.2 1.0
CG A:PRO1097 4.3 35.3 1.0
CB A:ILE1086 4.4 23.3 1.0
HG23 A:ILE1086 4.4 28.1 1.0
CB A:CYS1090 4.4 25.9 1.0
HG11 A:VAL1102 4.4 27.4 1.0
CA A:PRO1097 4.4 31.8 1.0
HD2 A:O371302 4.5 24.7 1.0
HG2 A:PRO1097 4.5 42.3 1.0
HD1 A:O371302 4.5 25.4 1.0
CG A:GLN1087 4.6 36.0 1.0
CA A:ILE1086 4.8 22.9 1.0
CD A:GLN1087 4.8 38.5 1.0
O A:ILE1083 4.8 31.1 1.0
O A:PRO1097 4.8 34.9 1.0
HB3 A:CYS1090 4.8 31.1 1.0
C A:GLN1087 4.8 25.8 1.0
HB3 A:GLN1087 4.9 36.5 1.0
OE1 A:GLN1087 4.9 40.7 1.0

Reference:

H.S.Kim, J.T.Hammill, D.C.Scott, Y.Chen, J.Min, J.Rector, B.Singh, B.A.Schulman, R.K.Guy. Discovery of Novel Pyrazolo-Pyridone DCN1 Inhibitors Controlling Cullin Neddylation. J.Med.Chem. V. 62 8429 2019.
ISSN: ISSN 0022-2623
PubMed: 31465221
DOI: 10.1021/ACS.JMEDCHEM.9B00410
Page generated: Fri Aug 2 00:06:36 2024

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