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Fluorine in PDB 5nk4: Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2C

Enzymatic activity of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2C

All present enzymatic activity of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2C:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2C, PDB code: 5nk4 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) 38.43 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 32.747, 107.910, 40.630, 90.00, 108.93, 90.00
R / Rfree (%) 16.9 / 19.7

Other elements in 5nk4:

The structure of Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2C 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 2C (pdb code 5nk4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2C, PDB code: 5nk4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5nk4

Go back to Fluorine Binding Sites List in 5nk4
Fluorine binding site 1 out of 4 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2C


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 2C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:39.0
occ:0.43
 FAX A:90E1001 0.0 39.0 0.4
CAW A:90E1001 1.3 34.8 0.4
FAY A:90E1001 2.1 34.5 0.4
CAR A:90E1001 2.3 36.8 0.4
CAV A:90E1001 2.3 30.4 0.4
NAQ A:90E1001 2.6 29.1 0.4
O A:ASN697 3.0 12.1 1.0
C A:ASN697 3.2 9.7 1.0
O A:HOH1295 3.3 43.0 1.0
O A:HOH1227 3.4 31.1 1.0
O A:HOH1184 3.4 18.7 1.0
NAU A:90E1001 3.6 48.8 0.4
CAS A:90E1001 3.6 25.5 0.4
CA A:ASN697 3.7 12.0 1.0
N A:GLY698 3.7 10.4 1.0
CAP A:90E1001 3.8 32.3 0.4
O A:GLU696 3.9 15.5 1.0
CA A:GLY698 3.9 10.1 1.0
CAT A:90E1001 4.0 32.2 0.4
CAM A:90E1001 4.1 21.1 0.6
CAN A:90E1001 4.3 20.9 0.6
CAO A:90E1001 4.4 21.8 0.4
O A:HOH1105 4.5 37.6 1.0
OAZ A:90E1001 4.6 43.2 0.4
N A:ASN697 4.6 11.3 1.0
C A:GLU696 4.7 14.7 1.0
CB A:ASN697 4.8 9.9 1.0
CAN A:90E1001 4.8 14.0 0.4
CAL A:90E1001 4.9 15.4 0.6
C A:GLY698 5.0 8.3 1.0

Fluorine binding site 2 out of 4 in 5nk4

Go back to Fluorine Binding Sites List in 5nk4
Fluorine binding site 2 out of 4 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2C


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 2C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:33.8
occ:0.57
 FAX A:90E1001 0.0 33.8 0.6
CAW A:90E1001 1.3 41.7 0.6
FAY A:90E1001 2.1 43.9 0.6
CAR A:90E1001 2.3 49.4 0.6
CAV A:90E1001 2.4 31.4 0.6
NAQ A:90E1001 2.6 40.0 0.6
SBB A:90E1001 3.3 10.4 0.6
OBC A:90E1001 3.5 13.4 0.6
SBB A:90E1001 3.5 16.3 0.4
CAS A:90E1001 3.6 35.5 0.6
NAU A:90E1001 3.6 58.7 0.6
CAL A:90E1001 3.6 11.7 0.4
OBC A:90E1001 3.7 15.5 0.4
CAM A:90E1001 3.8 18.4 0.4
CAP A:90E1001 4.0 22.9 0.6
CAT A:90E1001 4.1 36.4 0.6
CG1 A:VAL627 4.2 19.9 1.0
CBA A:90E1001 4.2 15.5 0.6
O A:HOH1323 4.3 41.8 1.0
CAF A:90E1001 4.4 10.5 0.6
CAE A:90E1001 4.4 15.1 0.6
CAO A:90E1001 4.5 16.5 0.6
CG2 A:VAL627 4.5 21.6 1.0
CB A:VAL627 4.5 14.7 1.0
O A:HOH1206 4.5 34.4 1.0
CAF A:90E1001 4.6 12.9 0.4
CAE A:90E1001 4.6 13.4 0.4
CAK A:90E1001 4.8 12.5 0.4
O A:HOH1217 4.8 31.4 1.0
CD1 A:ILE619 4.8 24.6 1.0
CAI A:90E1001 4.8 11.6 0.4
CAI A:90E1001 4.9 12.0 0.6
OAZ A:90E1001 4.9 20.0 0.6
O A:HOH1296 4.9 38.6 1.0
O A:ILE619 4.9 37.8 1.0
CG1 A:ILE619 5.0 19.5 1.0

Fluorine binding site 3 out of 4 in 5nk4

Go back to Fluorine Binding Sites List in 5nk4
Fluorine binding site 3 out of 4 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2C


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 2C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:34.5
occ:0.43
 FAY A:90E1001 0.0 34.5 0.4
CAW A:90E1001 1.4 34.8 0.4
FAX A:90E1001 2.1 39.0 0.4
O A:HOH1295 2.3 43.0 1.0
CAV A:90E1001 2.4 30.4 0.4
CAR A:90E1001 2.4 36.8 0.4
NAQ A:90E1001 2.7 29.1 0.4
CAT A:90E1001 2.9 32.2 0.4
NAU A:90E1001 2.9 48.8 0.4
CAP A:90E1001 3.1 32.3 0.4
CAS A:90E1001 3.2 25.5 0.4
OAZ A:90E1001 3.5 43.2 0.4
CAN A:90E1001 3.6 20.9 0.6
CAM A:90E1001 3.8 21.1 0.6
CAO A:90E1001 4.0 21.8 0.4
CAN A:90E1001 4.1 14.0 0.4
O A:HOH1184 4.2 18.7 1.0
O A:HOH1227 4.2 31.1 1.0
CAO A:90E1001 4.7 16.5 0.6
O A:ASN697 4.8 12.1 1.0
CA A:GLY698 5.0 10.1 1.0

Fluorine binding site 4 out of 4 in 5nk4

Go back to Fluorine Binding Sites List in 5nk4
Fluorine binding site 4 out of 4 in the Crystal Structure of Ephrin A2 (EPHA2) Receptor Protein Kinase with Compound 2C


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 2C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:43.9
occ:0.57
 FAY A:90E1001 0.0 43.9 0.6
CAW A:90E1001 1.3 41.7 0.6
FAX A:90E1001 2.1 33.8 0.6
CAR A:90E1001 2.3 49.4 0.6
CAV A:90E1001 2.4 31.4 0.6
NAQ A:90E1001 2.7 40.0 0.6
CAS A:90E1001 2.8 35.5 0.6
NAU A:90E1001 2.9 58.7 0.6
O A:ILE619 3.0 37.8 1.0
CA A:GLY620 3.3 37.5 1.0
CAT A:90E1001 3.4 36.4 0.6
C A:ILE619 3.6 34.2 1.0
N A:GLY620 3.7 26.4 1.0
CAM A:90E1001 3.7 18.4 0.4
CAP A:90E1001 3.8 22.9 0.6
CAL A:90E1001 4.2 11.7 0.4
CG1 A:ILE619 4.3 19.5 1.0
CB A:VAL627 4.4 14.7 1.0
CAO A:90E1001 4.4 16.5 0.6
CG1 A:VAL627 4.6 19.9 1.0
CG2 A:VAL627 4.6 21.6 1.0
OAZ A:90E1001 4.6 20.0 0.6
C A:GLY620 4.6 53.1 1.0
CAN A:90E1001 4.6 14.0 0.4
CB A:ILE619 4.7 24.4 1.0
CD1 A:ILE619 4.7 24.6 1.0
CBA A:90E1001 4.7 15.5 0.6
CA A:ILE619 4.8 27.8 1.0
SBB A:90E1001 4.9 10.4 0.6

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: Thu Aug 1 12:03:45 2024

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