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

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

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

Protein crystallography data

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

Resolution Low / High (Å) 37.08 / 1.57
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.233, 97.057, 59.837, 90, 106.11, 90
R / Rfree (%) 17 / 21

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of DCN1 Bound to N-((4S,5S)-3-(Aminomethyl)-7-Ethyl-4-(4- Fluorophenyl)-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4- B]Pyridin-5-Yl)-3-(Trifluoromethyl)Benzamide (pdb code 7kwa). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of DCN1 Bound to N-((4S,5S)-3-(Aminomethyl)-7-Ethyl-4-(4- Fluorophenyl)-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4- B]Pyridin-5-Yl)-3-(Trifluoromethyl)Benzamide, PDB code: 7kwa:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7kwa

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


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)-3-(Aminomethyl)-7-Ethyl-4-(4- Fluorophenyl)-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4- B]Pyridin-5-Yl)-3-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:51.6
occ:1.00
 F01 A:YHP1301 0.0 51.6 1.0
C02 A:YHP1301 1.4 51.9 1.0
C05 A:YHP1301 2.4 51.8 1.0
C03 A:YHP1301 2.4 51.4 1.0
HG22 A:ILE1086 2.5 31.0 1.0
H051 A:YHP1301 2.6 62.1 1.0
H031 A:YHP1301 2.6 61.7 1.0
HB3 A:PRO1097 2.8 36.5 1.0
HA A:GLN1087 3.0 30.6 1.0
HG A:CYS1090 3.0 29.5 1.0
HB2 A:PRO1097 3.2 36.5 1.0
CG2 A:ILE1086 3.4 25.8 1.0
CB A:PRO1097 3.5 30.4 1.0
HG21 A:ILE1086 3.6 31.0 1.0
SG A:CYS1090 3.6 24.6 1.0
C06 A:YHP1301 3.7 50.6 1.0
C04 A:YHP1301 3.7 50.3 1.0
N A:GLN1087 3.7 23.4 1.0
CA A:GLN1087 3.7 25.5 1.0
O A:ILE1086 3.8 22.5 1.0
C A:ILE1086 3.8 22.3 1.0
HB2 A:GLN1087 3.9 36.1 1.0
HB A:ILE1086 3.9 28.5 1.0
HB2 A:CYS1090 4.0 26.4 1.0
HA A:PRO1097 4.0 36.2 1.0
H A:GLN1087 4.1 28.1 1.0
HG23 A:ILE1086 4.1 31.0 1.0
C07 A:YHP1301 4.1 48.8 1.0
CB A:ILE1086 4.2 23.8 1.0
CA A:PRO1097 4.3 30.1 1.0
HD12 A:ILE1083 4.4 47.4 1.0
CB A:GLN1087 4.4 30.1 1.0
H061 A:YHP1301 4.4 60.7 1.0
H041 A:YHP1301 4.4 60.4 1.0
O A:PRO1097 4.4 32.3 1.0
CB A:CYS1090 4.4 22.0 1.0
HG11 A:VAL1102 4.5 30.7 1.0
CA A:ILE1086 4.6 23.3 1.0
HG3 A:PRO1097 4.7 37.9 1.0
CG A:PRO1097 4.7 31.6 1.0
CD A:GLN1087 4.9 39.0 1.0
C A:PRO1097 4.9 32.2 1.0
HB3 A:CYS1090 4.9 26.4 1.0
OE1 A:GLN1087 4.9 41.2 1.0
C A:GLN1087 4.9 25.0 1.0
HD11 A:ILE1083 4.9 47.4 1.0
H A:CYS1090 5.0 24.6 1.0
NE2 A:GLN1087 5.0 39.3 1.0

Fluorine binding site 2 out of 4 in 7kwa

Go back to Fluorine Binding Sites List in 7kwa
Fluorine binding site 2 out of 4 in the Structure of DCN1 Bound to N-((4S,5S)-3-(Aminomethyl)-7-Ethyl-4-(4- Fluorophenyl)-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4- B]Pyridin-5-Yl)-3-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of DCN1 Bound to N-((4S,5S)-3-(Aminomethyl)-7-Ethyl-4-(4- Fluorophenyl)-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4- B]Pyridin-5-Yl)-3-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:45.6
occ:1.00
 F18 A:YHP1301 0.0 45.6 1.0
C17 A:YHP1301 1.4 44.4 1.0
F20 A:YHP1301 2.2 43.6 1.0
F19 A:YHP1301 2.2 45.8 1.0
C16 A:YHP1301 2.3 40.8 1.0
H151 A:YHP1301 2.4 48.4 1.0
HG22 A:ILE1105 2.5 27.8 1.0
C15 A:YHP1301 2.7 40.3 1.0
HA A:ALA1106 3.1 21.8 1.0
CG2 A:ILE1105 3.4 23.2 1.0
CE2 A:PHE1117 3.5 24.4 1.0
HE2 A:PHE1117 3.5 29.3 1.0
HE2 A:PHE1089 3.5 27.1 1.0
HG21 A:ILE1105 3.6 27.8 1.0
CZ A:PHE1117 3.6 26.0 1.0
C21 A:YHP1301 3.6 38.8 1.0
HZ A:PHE1117 3.7 31.2 1.0
N A:ALA1106 3.8 19.3 1.0
HB2 A:ALA1106 3.8 21.7 1.0
CA A:ALA1106 3.8 18.2 1.0
HB2 A:PHE1109 3.9 26.1 1.0
HB A:ILE1105 3.9 27.1 1.0
H211 A:YHP1301 3.9 46.5 1.0
HG23 A:ILE1105 4.0 27.8 1.0
H A:ALA1106 4.0 23.2 1.0
CD2 A:PHE1117 4.0 23.1 1.0
C A:ILE1105 4.0 19.3 1.0
C14 A:YHP1301 4.1 39.0 1.0
CE2 A:PHE1089 4.2 22.6 1.0
CB A:ILE1105 4.2 22.6 1.0
CE1 A:PHE1117 4.2 25.4 1.0
HD1 A:PHE1109 4.2 29.2 1.0
O A:ILE1105 4.2 20.6 1.0
CD1 A:PHE1109 4.3 24.4 1.0
CB A:ALA1106 4.3 18.1 1.0
HD2 A:PHE1117 4.3 27.8 1.0
CG A:PHE1109 4.4 21.6 1.0
HD2 A:PHE1089 4.5 26.5 1.0
CB A:PHE1109 4.5 21.8 1.0
CG A:PHE1117 4.6 22.5 1.0
H141 A:YHP1301 4.6 46.8 1.0
HE1 A:PHE1117 4.6 30.5 1.0
CD1 A:PHE1117 4.7 24.9 1.0
HB1 A:ALA1106 4.7 21.7 1.0
CD2 A:PHE1089 4.7 22.1 1.0
C12 A:YHP1301 4.7 38.5 1.0
O A:VAL1102 4.8 19.1 1.0
HB3 A:PHE1109 4.8 26.1 1.0
CA A:ILE1105 4.8 19.8 1.0
CE1 A:PHE1109 4.8 25.3 1.0
HB2 A:ALA1111 4.8 24.8 1.0
HG13 A:VAL1102 4.8 30.7 1.0
C13 A:YHP1301 4.9 36.4 1.0
HZ A:PHE1089 5.0 27.5 1.0
CZ A:PHE1089 5.0 22.9 1.0

Fluorine binding site 3 out of 4 in 7kwa

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


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of DCN1 Bound to N-((4S,5S)-3-(Aminomethyl)-7-Ethyl-4-(4- Fluorophenyl)-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4- B]Pyridin-5-Yl)-3-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:45.8
occ:1.00
 F19 A:YHP1301 0.0 45.8 1.0
C17 A:YHP1301 1.4 44.4 1.0
F20 A:YHP1301 2.2 43.6 1.0
F18 A:YHP1301 2.2 45.6 1.0
C16 A:YHP1301 2.3 40.8 1.0
HD2 A:PHE1089 2.7 26.5 1.0
HE2 A:PHE1089 2.9 27.1 1.0
C21 A:YHP1301 3.2 38.8 1.0
CD2 A:PHE1089 3.2 22.1 1.0
C15 A:YHP1301 3.2 40.3 1.0
H211 A:YHP1301 3.2 46.5 1.0
H151 A:YHP1301 3.3 48.4 1.0
HG23 A:ILE1086 3.3 31.0 1.0
CE2 A:PHE1089 3.3 22.6 1.0
HE2 A:PHE1117 3.6 29.3 1.0
HD2 A:PHE1117 3.7 27.8 1.0
CE2 A:PHE1117 3.8 24.4 1.0
HG22 A:ILE1105 3.8 27.8 1.0
HG13 A:VAL1102 3.9 30.7 1.0
CD2 A:PHE1117 3.9 23.1 1.0
HG12 A:ILE1086 4.2 28.1 1.0
HG21 A:ILE1105 4.2 27.8 1.0
CG2 A:ILE1086 4.2 25.8 1.0
C12 A:YHP1301 4.4 38.5 1.0
CG A:PHE1089 4.4 22.0 1.0
C14 A:YHP1301 4.4 39.0 1.0
HG21 A:ILE1086 4.5 31.0 1.0
CG2 A:ILE1105 4.5 23.2 1.0
HB3 A:PHE1089 4.5 24.4 1.0
CZ A:PHE1089 4.5 22.9 1.0
HB A:ILE1105 4.5 27.1 1.0
CZ A:PHE1117 4.6 26.0 1.0
HA A:ILE1086 4.7 27.9 1.0
HG22 A:ILE1086 4.7 31.0 1.0
CG1 A:VAL1102 4.7 25.6 1.0
HG11 A:VAL1102 4.7 30.7 1.0
HB2 A:ALA1106 4.8 21.7 1.0
HD13 A:ILE1086 4.8 29.1 1.0
CG A:PHE1117 4.8 22.5 1.0
HZ A:PHE1089 4.9 27.5 1.0
HZ A:PHE1117 4.9 31.2 1.0
C13 A:YHP1301 4.9 36.4 1.0
CG1 A:ILE1086 5.0 23.4 1.0

Fluorine binding site 4 out of 4 in 7kwa

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


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of DCN1 Bound to N-((4S,5S)-3-(Aminomethyl)-7-Ethyl-4-(4- Fluorophenyl)-6-Oxo-1-Phenyl-4,5,6,7-Tetrahydro-1H-Pyrazolo[3,4- B]Pyridin-5-Yl)-3-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:43.6
occ:1.00
 F20 A:YHP1301 0.0 43.6 1.0
C17 A:YHP1301 1.4 44.4 1.0
F18 A:YHP1301 2.2 45.6 1.0
F19 A:YHP1301 2.2 45.8 1.0
C16 A:YHP1301 2.4 40.8 1.0
H211 A:YHP1301 2.6 46.5 1.0
HG13 A:VAL1102 2.7 30.7 1.0
C21 A:YHP1301 2.8 38.8 1.0
HB A:ILE1105 2.9 27.1 1.0
O A:VAL1102 2.9 19.1 1.0
HG22 A:ILE1105 3.0 27.8 1.0
H A:ALA1106 3.1 23.2 1.0
HB2 A:ALA1106 3.1 21.7 1.0
N A:ALA1106 3.4 19.3 1.0
C15 A:YHP1301 3.6 40.3 1.0
CG2 A:ILE1105 3.6 23.2 1.0
CG1 A:VAL1102 3.6 25.6 1.0
CB A:ILE1105 3.6 22.6 1.0
HA A:ALA1106 3.7 21.8 1.0
HG21 A:ILE1105 3.7 27.8 1.0
HG12 A:VAL1102 3.8 30.7 1.0
HA A:VAL1102 3.8 26.0 1.0
H151 A:YHP1301 3.8 48.4 1.0
C A:VAL1102 3.9 19.7 1.0
CA A:ALA1106 3.9 18.2 1.0
CB A:ALA1106 3.9 18.1 1.0
HE2 A:PHE1089 3.9 27.1 1.0
C A:ILE1105 4.0 19.3 1.0
HG11 A:VAL1102 4.0 30.7 1.0
C12 A:YHP1301 4.2 38.5 1.0
HD12 A:ILE1105 4.2 28.1 1.0
CA A:VAL1102 4.3 21.7 1.0
CA A:ILE1105 4.4 19.8 1.0
HD2 A:PHE1089 4.4 26.5 1.0
H101 A:YHP1301 4.4 48.9 1.0
HB3 A:ALA1106 4.4 21.7 1.0
HG23 A:ILE1105 4.5 27.8 1.0
CB A:VAL1102 4.6 24.8 1.0
HB1 A:ALA1106 4.6 21.7 1.0
CE2 A:PHE1089 4.7 22.6 1.0
HG23 A:ILE1086 4.7 31.0 1.0
H A:ILE1105 4.7 22.1 1.0
C14 A:YHP1301 4.7 39.0 1.0
CG1 A:ILE1105 4.8 23.4 1.0
O A:ILE1105 4.8 20.6 1.0
CD1 A:ILE1105 4.9 23.4 1.0
N A:ILE1105 4.9 18.4 1.0
CD2 A:PHE1089 4.9 22.1 1.0
HA A:LEU1103 4.9 23.8 1.0
C13 A:YHP1301 5.0 36.4 1.0
HD13 A:ILE1105 5.0 28.1 1.0

Reference:

H.S.Kim, J.T.Hammill, D.C.Scott, Y.Chen, A.L.Rice, W.Pistel, B.Singh, B.A.Schulman, R.K.Guy. Improvement of Oral Bioavailability of Pyrazolo-Pyridone Inhibitors of the Interaction of DCN1/2 and UBE2M. J.Med.Chem. V. 64 5850 2021.
ISSN: ISSN 0022-2623
PubMed: 33945681
DOI: 10.1021/ACS.JMEDCHEM.1C00035
Page generated: Fri Aug 2 08:32:25 2024

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