Fluorine in PDB 5ek0: Human NAV1.7-VSD4-Navab in Complex with Gx-936.

The structure of Human NAV1.7-VSD4-Navab in Complex with Gx-936., PDB code: 5ek0 was solved by S.Ahuja, S.Mukund, M.A.Starovasnik, C.M.Koth, J.Payandeh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.59 / 3.53
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	169.420, 188.830, 171.130, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 27.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Human NAV1.7-VSD4-Navab in Complex with Gx-936. (pdb code 5ek0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Human NAV1.7-VSD4-Navab in Complex with Gx-936., PDB code: 5ek0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the Human NAV1.7-VSD4-Navab in Complex with Gx-936.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human NAV1.7-VSD4-Navab in Complex with Gx-936. within 5.0Å range: probe atom residue distance (Å) B Occ A:F1808 b:0.9 occ:1.00 F37 A:5P21808 0.0 0.9 1.0 C36 A:5P21808 1.4 0.5 1.0 F39 A:5P21808 2.3 0.1 1.0 F38 A:5P21808 2.3 0.6 1.0 C14 A:5P21808 2.4 0.2 1.0 C13 A:5P21808 3.0 0.0 1.0 C15 A:5P21808 3.4 0.0 1.0 C23 A:PX41807 3.6 0.1 1.0 O7 A:PX41807 3.7 0.5 1.0 CH2 A:TRP1538 4.1 0.7 1.0 C12 A:5P21808 4.3 0.6 1.0 C16 A:5P21808 4.6 0.3 1.0 CZ3 A:TRP1538 4.7 0.2 1.0 CZ2 A:TRP1538 4.8 0.8 1.0 C17 A:5P21808 4.9 0.6 1.0 CE1 A:PHE1583 5.0 93.4 1.0

Fluorine binding site 2 out of 12 in the Human NAV1.7-VSD4-Navab in Complex with Gx-936.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human NAV1.7-VSD4-Navab in Complex with Gx-936. within 5.0Å range: probe atom residue distance (Å) B Occ A:F1808 b:0.6 occ:1.00 F38 A:5P21808 0.0 0.6 1.0 C36 A:5P21808 1.4 0.5 1.0 F39 A:5P21808 2.3 0.1 1.0 F37 A:5P21808 2.3 0.9 1.0 C14 A:5P21808 2.4 0.2 1.0 C15 A:5P21808 2.7 0.0 1.0 CE1 A:PHE1583 3.1 93.4 1.0 C13 A:5P21808 3.7 0.0 1.0 CD1 A:PHE1583 3.9 98.6 1.0 CZ A:PHE1583 4.0 99.1 1.0 C16 A:5P21808 4.1 0.3 1.0 SD A:MET1582 4.2 0.7 1.0 CG A:MET1582 4.4 98.1 1.0 CG1 A:VAL1541 4.7 0.2 1.0 CE A:MET1582 4.8 0.3 1.0 C12 A:5P21808 4.8 0.6 1.0 C17 A:5P21808 5.0 0.6 1.0

Fluorine binding site 3 out of 12 in the Human NAV1.7-VSD4-Navab in Complex with Gx-936.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human NAV1.7-VSD4-Navab in Complex with Gx-936. within 5.0Å range: probe atom residue distance (Å) B Occ A:F1808 b:0.1 occ:1.00 F39 A:5P21808 0.0 0.1 1.0 C36 A:5P21808 1.4 0.5 1.0 F38 A:5P21808 2.3 0.6 1.0 F37 A:5P21808 2.3 0.9 1.0 C14 A:5P21808 2.4 0.2 1.0 C13 A:5P21808 2.9 0.0 1.0 CH2 A:TRP1538 3.2 0.7 1.0 CZ3 A:TRP1538 3.2 0.2 1.0 C15 A:5P21808 3.5 0.0 1.0 CG1 A:VAL1541 3.5 0.2 1.0 C12 A:5P21808 4.3 0.6 1.0 CG2 A:VAL1541 4.3 97.4 1.0 CZ2 A:TRP1538 4.4 0.8 1.0 CE3 A:TRP1538 4.4 0.7 1.0 CB A:VAL1541 4.5 95.7 1.0 C16 A:5P21808 4.7 0.3 1.0 SD A:MET1582 5.0 0.7 1.0 C17 A:5P21808 5.0 0.6 1.0

Fluorine binding site 4 out of 12 in the Human NAV1.7-VSD4-Navab in Complex with Gx-936.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human NAV1.7-VSD4-Navab in Complex with Gx-936. within 5.0Å range: probe atom residue distance (Å) B Occ B:F1806 b:0.7 occ:1.00 F37 B:5P21806 0.0 0.7 1.0 C36 B:5P21806 1.4 0.5 1.0 F38 B:5P21806 2.3 0.5 1.0 F39 B:5P21806 2.3 0.3 1.0 C14 B:5P21806 2.4 0.5 1.0 C15 B:5P21806 2.8 0.3 1.0 CE1 B:PHE1583 3.1 0.2 1.0 C11 B:PX41805 3.5 0.8 1.0 C13 B:5P21806 3.7 0.3 1.0 CD1 B:PHE1583 3.9 0.3 1.0 CZ B:PHE1583 3.9 0.1 1.0 C12 B:PX41805 4.1 0.7 1.0 CE B:MET1582 4.1 0.3 1.0 C16 B:5P21806 4.1 0.1 1.0 C13 B:PX41805 4.2 0.6 1.0 C10 B:PX41805 4.3 0.4 1.0 C9 B:PX41805 4.3 0.9 1.0 O5 B:PX41805 4.5 0.7 1.0 C14 B:PX41805 4.8 0.4 1.0 C12 B:5P21806 4.8 1.0 1.0 O6 B:PX41805 4.8 0.7 1.0 C17 B:5P21806 5.0 0.7 1.0

Fluorine binding site 5 out of 12 in the Human NAV1.7-VSD4-Navab in Complex with Gx-936.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human NAV1.7-VSD4-Navab in Complex with Gx-936. within 5.0Å range: probe atom residue distance (Å) B Occ B:F1806 b:0.5 occ:1.00 F38 B:5P21806 0.0 0.5 1.0 C36 B:5P21806 1.4 0.5 1.0 F37 B:5P21806 2.3 0.7 1.0 F39 B:5P21806 2.3 0.3 1.0 C14 B:5P21806 2.4 0.5 1.0 C13 B:5P21806 3.2 0.3 1.0 C15 B:5P21806 3.2 0.3 1.0 CG1 B:VAL1541 3.4 89.9 1.0 CE B:MET1582 3.4 0.3 1.0 CZ3 B:TRP1538 3.6 89.5 1.0 CG2 B:VAL1541 4.0 95.0 1.0 CH2 B:TRP1538 4.1 87.0 1.0 CB B:VAL1541 4.3 94.2 1.0 C12 B:5P21806 4.4 1.0 1.0 C16 B:5P21806 4.4 0.1 1.0 CE3 B:TRP1538 4.6 91.7 1.0 CE1 B:PHE1583 4.7 0.2 1.0 C17 B:5P21806 4.9 0.7 1.0

Fluorine binding site 6 out of 12 in the Human NAV1.7-VSD4-Navab in Complex with Gx-936.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human NAV1.7-VSD4-Navab in Complex with Gx-936. within 5.0Å range: probe atom residue distance (Å) B Occ B:F1806 b:0.3 occ:1.00 F39 B:5P21806 0.0 0.3 1.0 C36 B:5P21806 1.4 0.5 1.0 F37 B:5P21806 2.3 0.7 1.0 F38 B:5P21806 2.3 0.5 1.0 C14 B:5P21806 2.4 0.5 1.0 C13 B:5P21806 2.8 0.3 1.0 CH2 B:TRP1538 3.2 87.0 1.0 O5 B:PX41805 3.4 0.7 1.0 CZ3 B:TRP1538 3.6 89.5 1.0 C15 B:5P21806 3.6 0.3 1.0 C11 B:PX41805 3.9 0.8 1.0 C10 B:PX41805 3.9 0.4 1.0 C9 B:PX41805 3.9 0.9 1.0 CZ2 B:TRP1538 4.2 90.1 1.0 C12 B:5P21806 4.2 1.0 1.0 C12 B:PX41805 4.4 0.7 1.0 C7 B:PX41805 4.6 0.5 1.0 C8 B:PX41805 4.6 0.6 1.0 C16 B:5P21806 4.8 0.1 1.0 CE3 B:TRP1538 4.8 91.7 1.0 O6 B:PX41805 4.9 0.7 1.0 C17 B:5P21806 5.0 0.7 1.0

Fluorine binding site 7 out of 12 in the Human NAV1.7-VSD4-Navab in Complex with Gx-936.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Human NAV1.7-VSD4-Navab in Complex with Gx-936. within 5.0Å range: probe atom residue distance (Å) B Occ C:F1805 b:0.2 occ:1.00 F37 C:5P21805 0.0 0.2 1.0 C36 C:5P21805 1.4 0.2 1.0 F39 C:5P21805 2.3 0.1 1.0 F38 C:5P21805 2.3 1.0 1.0 C14 C:5P21805 2.4 0.5 1.0 C15 C:5P21805 2.9 0.5 1.0 CE1 C:PHE1583 3.2 99.6 1.0 C13 C:5P21805 3.4 0.7 1.0 CD1 C:PHE1583 3.7 0.1 1.0 OD2 C:ASP1586 4.0 92.0 1.0 C16 C:5P21805 4.2 0.4 1.0 C7 C:PX41804 4.3 0.5 1.0 CZ C:PHE1583 4.3 97.8 1.0 C12 C:5P21805 4.6 0.7 1.0 C8 C:PX41804 4.7 0.2 1.0 C17 C:5P21805 4.9 0.9 1.0 CG C:ASP1586 5.0 0.7 1.0

Fluorine binding site 8 out of 12 in the Human NAV1.7-VSD4-Navab in Complex with Gx-936.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Human NAV1.7-VSD4-Navab in Complex with Gx-936. within 5.0Å range: probe atom residue distance (Å) B Occ C:F1805 b:1.0 occ:1.00 F38 C:5P21805 0.0 1.0 1.0 C36 C:5P21805 1.4 0.2 1.0 F39 C:5P21805 2.3 0.1 1.0 F37 C:5P21805 2.3 0.2 1.0 C14 C:5P21805 2.4 0.5 1.0 C15 C:5P21805 2.9 0.5 1.0 C13 C:5P21805 3.5 0.7 1.0 CE1 C:PHE1583 3.5 99.6 1.0 CG1 C:VAL1541 4.0 90.9 1.0 CE C:MET1582 4.0 0.3 1.0 CZ C:PHE1583 4.1 97.8 1.0 C16 C:5P21805 4.2 0.4 1.0 SD C:MET1582 4.3 0.6 1.0 CZ3 C:TRP1538 4.3 0.5 1.0 CD1 C:PHE1583 4.4 0.1 1.0 CG2 C:VAL1541 4.5 89.6 1.0 C12 C:5P21805 4.6 0.7 1.0 CH2 C:TRP1538 4.7 0.5 1.0 CB C:VAL1541 4.9 91.7 1.0 C17 C:5P21805 4.9 0.9 1.0

Fluorine binding site 9 out of 12 in the Human NAV1.7-VSD4-Navab in Complex with Gx-936.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Human NAV1.7-VSD4-Navab in Complex with Gx-936. within 5.0Å range: probe atom residue distance (Å) B Occ C:F1805 b:0.1 occ:1.00 F39 C:5P21805 0.0 0.1 1.0 C36 C:5P21805 1.4 0.2 1.0 F37 C:5P21805 2.3 0.2 1.0 F38 C:5P21805 2.3 1.0 1.0 C14 C:5P21805 2.4 0.5 1.0 C13 C:5P21805 2.7 0.7 1.0 CH2 C:TRP1538 3.1 0.5 1.0 CZ3 C:TRP1538 3.4 0.5 1.0 C15 C:5P21805 3.7 0.5 1.0 C7 C:PX41804 3.8 0.5 1.0 C12 C:5P21805 4.1 0.7 1.0 CZ2 C:TRP1538 4.3 0.3 1.0 C6 C:PX41804 4.7 0.2 1.0 OD2 C:ASP1586 4.7 92.0 1.0 CE3 C:TRP1538 4.7 0.7 1.0 C16 C:5P21805 4.8 0.4 1.0 C8 C:PX41804 4.9 0.2 1.0 C17 C:5P21805 5.0 0.9 1.0

Fluorine binding site 10 out of 12 in the Human NAV1.7-VSD4-Navab in Complex with Gx-936.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Human NAV1.7-VSD4-Navab in Complex with Gx-936. within 5.0Å range: probe atom residue distance (Å) B Occ D:F1806 b:0.1 occ:1.00 F37 D:5P21806 0.0 0.1 1.0 C36 D:5P21806 1.4 0.9 1.0 F38 D:5P21806 2.3 0.6 1.0 F39 D:5P21806 2.3 0.1 1.0 C14 D:5P21806 2.4 0.3 1.0 C13 D:5P21806 3.1 0.7 1.0 C15 D:5P21806 3.3 0.8 1.0 C10 D:PX41805 3.4 0.3 1.0 O6 D:PX41805 3.4 0.8 1.0 C9 D:PX41805 3.6 0.3 1.0 C12 D:PX41805 4.0 0.6 1.0 C11 D:PX41805 4.0 0.4 1.0 CE1 D:PHE1583 4.3 99.3 1.0 C12 D:5P21806 4.3 0.0 1.0 CH2 D:TRP1538 4.4 98.6 1.0 C16 D:5P21806 4.5 0.8 1.0 O5 D:PX41805 4.6 0.6 1.0 OD2 D:ASP1586 4.7 0.7 1.0 C8 D:PX41805 4.7 0.7 1.0 CZ D:PHE1583 4.9 99.0 1.0 C17 D:5P21806 4.9 0.4 1.0

S.Ahuja, S.Mukund, L.Deng, K.Khakh, E.Chang, H.Ho, S.Shriver, C.Young, S.Lin, J.P.Johnson, P.Wu, J.Li, M.Coons, C.Tam, B.Brillantes, H.Sampang, K.Mortara, K.K.Bowman, K.R.Clark, A.Estevez, Z.Xie, H.Verschoof, M.Grimwood, C.Dehnhardt, J.C.Andrez, T.Focken, D.P.Sutherlin, B.S.Safina, M.A.Starovasnik, D.F.Ortwine, Y.Franke, C.J.Cohen, D.H.Hackos, C.M.Koth, J.Payandeh. Structural Basis of NAV1.7 Inhibition By An Isoform-Selective Small-Molecule Antagonist. Science V. 350 C5464 2015.
ISSN: ESSN 1095-9203
PubMed: 26680203
DOI: 10.1126/SCIENCE.AAC5464