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Fluorine in PDB 6fnj: Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712

Enzymatic activity of Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712

All present enzymatic activity of Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712, PDB code: 6fnj was solved by D.Kudlinzki, A.Troester, K.Witt, V.L.Linhard, K.Saxena, H.Schwalbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.34 / 1.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.820, 87.690, 81.742, 90.00, 104.95, 90.00
R / Rfree (%) 21 / 22.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712 (pdb code 6fnj). 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 Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712, PDB code: 6fnj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6fnj

Go back to Fluorine Binding Sites List in 6fnj
Fluorine binding site 1 out of 6 in the Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712


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 Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:30.2
occ:1.00
 FBI A:DWT1001 0.0 30.2 1.0
CBH A:DWT1001 1.3 32.1 1.0
FBJ A:DWT1001 2.0 30.8 1.0
FBK A:DWT1001 2.0 29.4 1.0
CBF A:DWT1001 2.2 28.1 1.0
CBG A:DWT1001 2.6 30.8 1.0
CE1 A:PHE671 3.4 36.6 1.0
CBD A:DWT1001 3.5 28.1 1.0
CE2 A:TYR736 3.7 27.3 1.0
CD1 A:LEU731 3.8 26.6 1.0
CD1 A:PHE671 3.9 36.9 1.0
CBE A:DWT1001 4.0 29.9 1.0
CD2 A:HIS738 4.2 26.8 1.0
CZ A:PHE671 4.2 33.2 1.0
CD2 A:LEU731 4.2 26.3 1.0
CD2 A:TYR736 4.3 27.7 1.0
CZ A:TYR736 4.4 31.1 1.0
O A:HOH1123 4.5 28.5 1.0
OH A:TYR736 4.5 30.6 1.0
CG2 A:ILE676 4.6 29.2 0.4
NE2 A:HIS738 4.6 26.7 1.0
CG A:LEU731 4.6 24.9 1.0
CBB A:DWT1001 4.7 30.4 1.0
CG2 A:ILE676 4.8 29.5 0.6
CG1 A:VAL756 4.8 26.2 1.0
CBC A:DWT1001 4.9 28.4 1.0

Fluorine binding site 2 out of 6 in 6fnj

Go back to Fluorine Binding Sites List in 6fnj
Fluorine binding site 2 out of 6 in the Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712


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 Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:30.8
occ:1.00
 FBJ A:DWT1001 0.0 30.8 1.0
CBH A:DWT1001 1.1 32.1 1.0
FBK A:DWT1001 1.9 29.4 1.0
FBI A:DWT1001 2.0 30.2 1.0
CBF A:DWT1001 2.0 28.1 1.0
CBD A:DWT1001 2.8 28.1 1.0
CBG A:DWT1001 3.1 30.8 1.0
C A:SER757 3.1 25.1 1.0
O A:SER757 3.3 24.3 1.0
CA A:SER757 3.4 22.4 1.0
NE2 A:HIS738 3.6 26.7 1.0
N A:ASP758 3.6 25.1 1.0
N A:SER757 3.7 24.3 1.0
CD2 A:HIS738 3.7 26.8 1.0
O A:VAL756 3.8 26.6 1.0
CG1 A:VAL756 3.8 26.2 1.0
C A:VAL756 3.9 27.2 1.0
CB A:ASP758 4.0 25.6 1.0
CBB A:DWT1001 4.1 30.4 1.0
CBE A:DWT1001 4.3 29.9 1.0
CA A:ASP758 4.4 23.0 1.0
CB A:VAL756 4.7 23.1 1.0
CBC A:DWT1001 4.7 28.4 1.0
OBA A:DWT1001 4.7 27.1 1.0
O A:HOH1123 4.8 28.5 1.0
CE1 A:HIS738 4.8 25.6 1.0
CB A:SER757 4.8 24.8 1.0
CD1 A:LEU731 4.8 26.6 1.0
CG2 A:ILE676 4.9 29.2 0.4
CA A:VAL756 4.9 24.1 1.0
CG A:HIS738 4.9 25.0 1.0
CG2 A:ILE677 5.0 27.9 0.4
CG2 A:ILE677 5.0 27.9 0.6

Fluorine binding site 3 out of 6 in 6fnj

Go back to Fluorine Binding Sites List in 6fnj
Fluorine binding site 3 out of 6 in the Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712


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 Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:29.4
occ:1.00
 FBK A:DWT1001 0.0 29.4 1.0
CBH A:DWT1001 1.1 32.1 1.0
FBJ A:DWT1001 1.9 30.8 1.0
FBI A:DWT1001 2.0 30.2 1.0
CBF A:DWT1001 2.1 28.1 1.0
CBD A:DWT1001 2.7 28.1 1.0
CBG A:DWT1001 3.3 30.8 1.0
CG2 A:ILE676 3.4 29.2 0.4
CG2 A:ILE676 3.6 29.5 0.6
O A:VAL756 3.6 26.6 1.0
CD1 A:PHE671 3.8 36.9 1.0
CE1 A:PHE671 3.9 36.6 1.0
CG2 A:ILE677 4.0 27.9 0.4
CBB A:DWT1001 4.0 30.4 1.0
CG2 A:ILE677 4.0 27.9 0.6
CA A:SER757 4.2 22.4 1.0
C A:VAL756 4.3 27.2 1.0
CBE A:DWT1001 4.4 29.9 1.0
C A:SER757 4.5 25.1 1.0
N A:SER757 4.6 24.3 1.0
CBC A:DWT1001 4.7 28.4 1.0
N A:ILE677 4.8 25.6 0.4
OBA A:DWT1001 4.8 27.1 1.0
CB A:ILE676 4.8 28.8 0.4
N A:ASP758 4.8 25.1 1.0
N A:ILE677 4.8 25.6 0.6
CG1 A:VAL756 4.8 26.2 1.0
CD1 A:ILE676 4.9 22.1 0.6
O A:SER757 4.9 24.3 1.0
CB A:ILE676 4.9 28.6 0.6
CG A:PHE671 5.0 35.3 1.0

Fluorine binding site 4 out of 6 in 6fnj

Go back to Fluorine Binding Sites List in 6fnj
Fluorine binding site 4 out of 6 in the Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712


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 Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:31.8
occ:1.00
 FBI B:DWT1001 0.0 31.8 1.0
CBH B:DWT1001 1.2 31.2 1.0
FBK B:DWT1001 1.9 30.2 1.0
FBJ B:DWT1001 2.0 31.7 1.0
CBF B:DWT1001 2.2 28.4 1.0
CBG B:DWT1001 2.6 33.1 1.0
CBD B:DWT1001 3.5 28.1 1.0
CE1 B:PHE671 3.5 41.6 1.0
CE2 B:TYR736 3.8 30.5 1.0
CD1 B:LEU731 3.9 27.0 1.0
CBE B:DWT1001 3.9 31.4 1.0
CD1 B:PHE671 4.0 42.7 1.0
CD2 B:LEU731 4.1 26.0 1.0
CD2 B:HIS738 4.2 26.6 1.0
CD2 B:TYR736 4.3 30.9 1.0
CZ B:PHE671 4.4 39.7 1.0
CZ B:TYR736 4.4 32.7 1.0
O B:HOH1129 4.5 29.7 1.0
OH B:TYR736 4.6 29.7 1.0
CG2 B:ILE676 4.6 29.8 0.2
CBB B:DWT1001 4.6 29.7 1.0
CG B:LEU731 4.6 28.0 1.0
NE2 B:HIS738 4.7 27.9 1.0
CG2 B:ILE676 4.7 29.8 0.8
CBC B:DWT1001 4.8 28.8 1.0
CG1 B:VAL756 4.8 26.1 1.0

Fluorine binding site 5 out of 6 in 6fnj

Go back to Fluorine Binding Sites List in 6fnj
Fluorine binding site 5 out of 6 in the Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712


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 Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:31.7
occ:1.00
 FBJ B:DWT1001 0.0 31.7 1.0
CBH B:DWT1001 1.2 31.2 1.0
FBK B:DWT1001 1.9 30.2 1.0
FBI B:DWT1001 2.0 31.8 1.0
CBF B:DWT1001 2.1 28.4 1.0
CBD B:DWT1001 2.9 28.1 1.0
CBG B:DWT1001 3.1 33.1 1.0
C B:SER757 3.2 25.3 1.0
O B:SER757 3.3 24.1 1.0
CA B:SER757 3.4 24.6 1.0
NE2 B:HIS738 3.6 27.9 1.0
N B:ASP758 3.7 25.3 1.0
N B:SER757 3.7 24.1 1.0
CD2 B:HIS738 3.7 26.6 1.0
O B:VAL756 3.7 26.2 1.0
CG1 B:VAL756 3.8 26.1 1.0
C B:VAL756 3.8 25.2 1.0
CB B:ASP758 4.0 28.7 1.0
CBB B:DWT1001 4.1 29.7 1.0
CBE B:DWT1001 4.3 31.4 1.0
CA B:ASP758 4.4 24.0 1.0
CB B:VAL756 4.7 23.2 1.0
CBC B:DWT1001 4.7 28.8 1.0
OBA B:DWT1001 4.7 27.8 1.0
O B:HOH1129 4.8 29.7 1.0
CE1 B:HIS738 4.8 26.4 1.0
CB B:SER757 4.8 25.4 1.0
CD1 B:LEU731 4.8 27.0 1.0
CA B:VAL756 4.9 24.3 1.0
CG2 B:ILE676 4.9 29.8 0.2
CG B:HIS738 4.9 23.6 1.0

Fluorine binding site 6 out of 6 in 6fnj

Go back to Fluorine Binding Sites List in 6fnj
Fluorine binding site 6 out of 6 in the Crystal Structure of Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712


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 Ephrin B4 (EPHB4) Receptor Protein Kinase with An Isomer of Nvp-BHG712 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:30.2
occ:1.00
 FBK B:DWT1001 0.0 30.2 1.0
CBH B:DWT1001 1.1 31.2 1.0
FBJ B:DWT1001 1.9 31.7 1.0
FBI B:DWT1001 1.9 31.8 1.0
CBF B:DWT1001 2.0 28.4 1.0
CBD B:DWT1001 2.6 28.1 1.0
CBG B:DWT1001 3.2 33.1 1.0
CG2 B:ILE676 3.5 29.8 0.2
CG2 B:ILE676 3.6 29.8 0.8
O B:VAL756 3.6 26.2 1.0
CD1 B:PHE671 4.0 42.7 1.0
CBB B:DWT1001 4.0 29.7 1.0
CG2 B:ILE677 4.1 29.7 1.0
CE1 B:PHE671 4.2 41.6 1.0
CA B:SER757 4.2 24.6 1.0
C B:VAL756 4.3 25.2 1.0
CBE B:DWT1001 4.4 31.4 1.0
C B:SER757 4.5 25.3 1.0
N B:SER757 4.6 24.1 1.0
CBC B:DWT1001 4.7 28.8 1.0
OBA B:DWT1001 4.8 27.8 1.0
CB B:ILE676 4.8 27.8 0.2
N B:ASP758 4.8 25.3 1.0
CD1 B:ILE676 4.8 26.9 0.8
N B:ILE677 4.9 26.7 1.0
CG1 B:VAL756 4.9 26.1 1.0
CB B:ILE676 4.9 27.4 0.8
O B:SER757 4.9 24.1 1.0
NAZ B:DWT1001 5.0 28.9 1.0

Reference:

A.Troster, S.Heinzlmeir, B.T.Berger, S.L.Gande, K.Saxena, S.Sreeramulu, V.Linhard, A.H.Nasiri, M.Bolte, S.Muller, B.Kuster, G.Medard, D.Kudlinzki, H.Schwalbe. Nvp-BHG712: Effects of Regioisomers on the Affinity and Selectivity Toward the Ephrin Family. Chemmedchem V. 13 1629 2018.
ISSN: ESSN 1860-7187
PubMed: 29928781
DOI: 10.1002/CMDC.201800398
Page generated: Thu Aug 1 20:09:43 2024

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