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Fluorine in PDB 5nkf: Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B

Enzymatic activity of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B

All present enzymatic activity of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B, PDB code: 5nkf was solved by D.Kudlinzki, V.L.Linhard, K.Witt, S.L.Gande, K.Saxena, S.Heinzlmeir, G.Medard, B.Kuester, H.Schwalbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.42 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 32.716, 107.726, 40.549, 90.00, 108.65, 90.00
R / Rfree (%) 17.1 / 18.7

Other elements in 5nkf:

The structure of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B (pdb code 5nkf). 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 A2 (EPHA2) Receptor Protein Kinase with Compound 3B, PDB code: 5nkf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5nkf

Go back to Fluorine Binding Sites List in 5nkf
Fluorine binding site 1 out of 6 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B


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 A2 (EPHA2) Receptor Protein Kinase with Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:27.8
occ:0.43
 FAP A:8ZN1001 0.0 27.8 0.4
FAP A:8ZN1001 0.0 27.4 0.6
CAN A:8ZN1001 1.2 22.5 0.6
CAN A:8ZN1001 1.2 21.9 0.4
FAO A:8ZN1001 1.7 27.8 0.4
FAO A:8ZN1001 1.7 26.5 0.6
FAQ A:8ZN1001 1.9 28.5 0.4
FAQ A:8ZN1001 1.9 28.2 0.6
CAM A:8ZN1001 2.2 17.1 0.6
CAM A:8ZN1001 2.2 17.5 0.4
CAR A:8ZN1001 2.7 18.2 0.6
CAR A:8ZN1001 2.7 18.7 0.4
O A:HOH1339 3.2 19.8 1.0
O A:HOH1420 3.3 27.1 1.0
CAL A:8ZN1001 3.5 12.4 0.6
CAL A:8ZN1001 3.5 12.2 0.4
O A:ILE619 3.6 27.7 1.0
O A:HOH1234 3.6 35.1 1.0
O A:HOH1368 4.0 31.0 1.0
CAS A:8ZN1001 4.0 18.2 0.6
CAS A:8ZN1001 4.0 18.2 0.4
C A:ILE619 4.6 26.3 1.0
CAK A:8ZN1001 4.7 12.9 0.6
CAK A:8ZN1001 4.7 12.3 0.4
CAT A:8ZN1001 4.9 25.0 0.6
CBC A:8ZN1001 4.9 12.9 0.6
CBC A:8ZN1001 4.9 15.6 0.4
CAT A:8ZN1001 4.9 24.9 0.4

Fluorine binding site 2 out of 6 in 5nkf

Go back to Fluorine Binding Sites List in 5nkf
Fluorine binding site 2 out of 6 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B


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 A2 (EPHA2) Receptor Protein Kinase with Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:27.4
occ:0.55
 FAP A:8ZN1001 0.0 27.4 0.6
FAP A:8ZN1001 0.0 27.8 0.4
CAN A:8ZN1001 1.2 22.5 0.6
CAN A:8ZN1001 1.2 21.9 0.4
FAO A:8ZN1001 1.7 27.8 0.4
FAO A:8ZN1001 1.7 26.5 0.6
FAQ A:8ZN1001 1.9 28.5 0.4
FAQ A:8ZN1001 1.9 28.2 0.6
CAM A:8ZN1001 2.2 17.1 0.6
CAM A:8ZN1001 2.2 17.5 0.4
CAR A:8ZN1001 2.7 18.2 0.6
CAR A:8ZN1001 2.7 18.7 0.4
O A:HOH1339 3.2 19.8 1.0
O A:HOH1420 3.3 27.1 1.0
CAL A:8ZN1001 3.5 12.4 0.6
CAL A:8ZN1001 3.5 12.2 0.4
O A:ILE619 3.6 27.7 1.0
O A:HOH1234 3.6 35.1 1.0
O A:HOH1368 4.0 31.0 1.0
CAS A:8ZN1001 4.0 18.2 0.6
CAS A:8ZN1001 4.0 18.2 0.4
C A:ILE619 4.6 26.3 1.0
CAK A:8ZN1001 4.7 12.9 0.6
CAK A:8ZN1001 4.7 12.3 0.4
CAT A:8ZN1001 4.9 25.0 0.6
CBC A:8ZN1001 4.9 12.9 0.6
CBC A:8ZN1001 4.9 15.6 0.4
CAT A:8ZN1001 4.9 24.9 0.4

Fluorine binding site 3 out of 6 in 5nkf

Go back to Fluorine Binding Sites List in 5nkf
Fluorine binding site 3 out of 6 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B


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 A2 (EPHA2) Receptor Protein Kinase with Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:28.5
occ:0.43
 FAQ A:8ZN1001 0.0 28.5 0.4
FAQ A:8ZN1001 0.0 28.2 0.6
CAN A:8ZN1001 1.3 22.5 0.6
CAN A:8ZN1001 1.3 21.9 0.4
FAO A:8ZN1001 1.8 26.5 0.6
FAO A:8ZN1001 1.8 27.8 0.4
FAP A:8ZN1001 1.9 27.4 0.6
FAP A:8ZN1001 1.9 27.8 0.4
CAM A:8ZN1001 2.2 17.1 0.6
CAM A:8ZN1001 2.2 17.5 0.4
CAL A:8ZN1001 2.9 12.4 0.6
CAL A:8ZN1001 2.9 12.2 0.4
CAR A:8ZN1001 3.3 18.2 0.6
CAR A:8ZN1001 3.3 18.7 0.4
O A:ILE619 3.6 27.7 1.0
O A:HOH1424 3.6 36.6 1.0
CAK A:8ZN1001 4.2 12.9 0.6
CAK A:8ZN1001 4.2 12.3 0.4
O A:HOH1278 4.3 34.3 1.0
C A:ILE619 4.3 26.3 1.0
SBD A:8ZN1001 4.4 11.0 0.6
SBD A:8ZN1001 4.4 8.9 0.4
CG1 A:ILE619 4.4 19.9 1.0
CAS A:8ZN1001 4.4 18.2 0.6
CAS A:8ZN1001 4.4 18.2 0.4
CD1 A:ILE619 4.6 19.1 1.0
O A:HOH1420 4.6 27.1 1.0
CB A:ILE619 4.6 20.8 1.0
O A:HOH1339 4.7 19.8 1.0
O A:HOH1234 4.8 35.1 1.0
CBC A:8ZN1001 4.8 15.6 0.4
CBC A:8ZN1001 4.8 12.9 0.6
N A:GLY620 4.8 22.0 1.0
CA A:GLY620 4.8 24.8 1.0

Fluorine binding site 4 out of 6 in 5nkf

Go back to Fluorine Binding Sites List in 5nkf
Fluorine binding site 4 out of 6 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B


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 A2 (EPHA2) Receptor Protein Kinase with Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:28.2
occ:0.55
 FAQ A:8ZN1001 0.0 28.5 0.4
FAQ A:8ZN1001 0.0 28.2 0.6
CAN A:8ZN1001 1.3 22.5 0.6
CAN A:8ZN1001 1.3 21.9 0.4
FAO A:8ZN1001 1.8 26.5 0.6
FAO A:8ZN1001 1.8 27.8 0.4
FAP A:8ZN1001 1.9 27.4 0.6
FAP A:8ZN1001 1.9 27.8 0.4
CAM A:8ZN1001 2.2 17.1 0.6
CAM A:8ZN1001 2.2 17.5 0.4
CAL A:8ZN1001 2.9 12.4 0.6
CAL A:8ZN1001 2.9 12.2 0.4
CAR A:8ZN1001 3.3 18.2 0.6
CAR A:8ZN1001 3.3 18.7 0.4
O A:ILE619 3.6 27.7 1.0
O A:HOH1424 3.6 36.6 1.0
CAK A:8ZN1001 4.2 12.9 0.6
CAK A:8ZN1001 4.2 12.3 0.4
O A:HOH1278 4.3 34.3 1.0
C A:ILE619 4.3 26.3 1.0
SBD A:8ZN1001 4.4 11.0 0.6
SBD A:8ZN1001 4.4 8.9 0.4
CG1 A:ILE619 4.4 19.9 1.0
CAS A:8ZN1001 4.4 18.2 0.6
CAS A:8ZN1001 4.4 18.2 0.4
CD1 A:ILE619 4.6 19.1 1.0
O A:HOH1420 4.6 27.1 1.0
CB A:ILE619 4.6 20.8 1.0
O A:HOH1339 4.7 19.8 1.0
O A:HOH1234 4.8 35.1 1.0
CBC A:8ZN1001 4.8 15.6 0.4
CBC A:8ZN1001 4.8 12.9 0.6
N A:GLY620 4.8 22.0 1.0
CA A:GLY620 4.8 24.8 1.0

Fluorine binding site 5 out of 6 in 5nkf

Go back to Fluorine Binding Sites List in 5nkf
Fluorine binding site 5 out of 6 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B


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 A2 (EPHA2) Receptor Protein Kinase with Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:27.8
occ:0.43
 FAO A:8ZN1001 0.0 27.8 0.4
FAO A:8ZN1001 0.0 26.5 0.6
CAN A:8ZN1001 0.9 21.9 0.4
CAN A:8ZN1001 0.9 22.5 0.6
FAP A:8ZN1001 1.7 27.4 0.6
FAP A:8ZN1001 1.7 27.8 0.4
FAQ A:8ZN1001 1.8 28.5 0.4
FAQ A:8ZN1001 1.8 28.2 0.6
CAM A:8ZN1001 2.1 17.1 0.6
CAM A:8ZN1001 2.1 17.5 0.4
CAL A:8ZN1001 2.8 12.4 0.6
CAL A:8ZN1001 2.8 12.2 0.4
CAR A:8ZN1001 3.2 18.2 0.6
CAR A:8ZN1001 3.2 18.7 0.4
O A:HOH1339 3.3 19.8 1.0
O A:HOH1420 3.4 27.1 1.0
N A:ALA699 4.1 7.6 1.0
CAK A:8ZN1001 4.1 12.9 0.6
CAK A:8ZN1001 4.1 12.3 0.4
CB A:ALA699 4.2 10.4 1.0
O A:HOH1424 4.2 36.6 1.0
CAS A:8ZN1001 4.4 18.2 0.6
CAS A:8ZN1001 4.4 18.2 0.4
O A:HOH1278 4.6 34.3 1.0
CA A:GLY698 4.6 9.3 1.0
CD2 A:LEU746 4.6 11.2 1.0
CA A:ALA699 4.7 8.2 1.0
CBC A:8ZN1001 4.8 12.9 0.6
CBC A:8ZN1001 4.8 15.6 0.4
C A:GLY698 4.8 7.9 1.0
SBD A:8ZN1001 4.9 11.0 0.6
SBD A:8ZN1001 4.9 8.9 0.4
O A:ILE619 4.9 27.7 1.0

Fluorine binding site 6 out of 6 in 5nkf

Go back to Fluorine Binding Sites List in 5nkf
Fluorine binding site 6 out of 6 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 3B


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 A2 (EPHA2) Receptor Protein Kinase with Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:26.5
occ:0.55
 FAO A:8ZN1001 0.0 26.5 0.6
FAO A:8ZN1001 0.0 27.8 0.4
CAN A:8ZN1001 0.9 21.9 0.4
CAN A:8ZN1001 0.9 22.5 0.6
FAP A:8ZN1001 1.7 27.4 0.6
FAP A:8ZN1001 1.7 27.8 0.4
FAQ A:8ZN1001 1.8 28.5 0.4
FAQ A:8ZN1001 1.8 28.2 0.6
CAM A:8ZN1001 2.1 17.1 0.6
CAM A:8ZN1001 2.1 17.5 0.4
CAL A:8ZN1001 2.8 12.4 0.6
CAL A:8ZN1001 2.8 12.2 0.4
CAR A:8ZN1001 3.2 18.2 0.6
CAR A:8ZN1001 3.2 18.7 0.4
O A:HOH1339 3.3 19.8 1.0
O A:HOH1420 3.4 27.1 1.0
N A:ALA699 4.1 7.6 1.0
CAK A:8ZN1001 4.1 12.9 0.6
CAK A:8ZN1001 4.1 12.3 0.4
CB A:ALA699 4.2 10.4 1.0
O A:HOH1424 4.2 36.6 1.0
CAS A:8ZN1001 4.4 18.2 0.6
CAS A:8ZN1001 4.4 18.2 0.4
O A:HOH1278 4.6 34.3 1.0
CA A:GLY698 4.6 9.3 1.0
CD2 A:LEU746 4.6 11.2 1.0
CA A:ALA699 4.7 8.2 1.0
CBC A:8ZN1001 4.8 12.9 0.6
CBC A:8ZN1001 4.8 15.6 0.4
C A:GLY698 4.8 7.9 1.0
SBD A:8ZN1001 4.9 11.0 0.6
SBD A:8ZN1001 4.9 8.9 0.4
O A:ILE619 4.9 27.7 1.0

Reference:

S.Heinzlmeir, J.Lohse, T.Treiber, D.Kudlinzki, V.Linhard, S.L.Gande, S.Sreeramulu, K.Saxena, X.Liu, M.Wilhelm, H.Schwalbe, B.Kuster, G.Medard. Chemoproteomics-Aided Medicinal Chemistry For the Discovery of EPHA2 Inhibitors. Chemmedchem V. 12 999 2017.
ISSN: ESSN 1860-7187
PubMed: 28544567
DOI: 10.1002/CMDC.201700217
Page generated: Tue Jul 15 05:30:25 2025

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