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Fluorine in PDB 6s41: Crystal Structure of Pxr in Complex with Xpc-7455

Protein crystallography data

The structure of Crystal Structure of Pxr in Complex with Xpc-7455, PDB code: 6s41 was solved by T.Focken, K.Maskos, A.Griessner, S.Krapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.11 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.318, 89.002, 105.815, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.9

Other elements in 6s41:

The structure of Crystal Structure of Pxr in Complex with Xpc-7455 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Pxr in Complex with Xpc-7455 (pdb code 6s41). 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 Pxr in Complex with Xpc-7455, PDB code: 6s41:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6s41

Go back to Fluorine Binding Sites List in 6s41
Fluorine binding site 1 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:75.1
occ:1.00
F22 A:KUB701 0.0 75.1 1.0
C21 A:KUB701 1.3 60.5 1.0
C20 A:KUB701 2.4 60.3 1.0
C23 A:KUB701 2.4 56.8 1.0
CD2 A:LEU324 3.4 38.2 1.0
CG A:MET323 3.5 50.8 1.0
C19 A:KUB701 3.6 58.5 1.0
C24 A:KUB701 3.7 54.4 1.0
CD2 A:LEU209 3.7 70.3 1.0
CE A:MET323 3.8 55.1 1.0
SD A:MET323 3.8 52.0 1.0
CH2 A:TRP299 3.9 27.1 1.0
CZ2 A:TRP299 4.0 26.8 1.0
CB A:MET323 4.1 44.8 1.0
C25 A:KUB701 4.1 55.0 1.0
CG A:LEU324 4.4 38.6 1.0
C A:MET323 4.4 35.4 1.0
O A:MET323 4.4 36.7 1.0
CD2 A:HIS327 4.5 25.0 1.0
N A:LEU324 4.6 34.9 1.0
CG A:LEU209 4.7 72.0 1.0
CD1 A:LEU209 4.8 77.0 1.0
CA A:LEU324 4.8 35.5 1.0
NE2 A:HIS327 4.9 24.4 1.0
C16 A:KUB701 4.9 54.5 1.0
CA A:MET323 4.9 38.7 1.0
CZ3 A:TRP299 4.9 26.6 1.0

Fluorine binding site 2 out of 6 in 6s41

Go back to Fluorine Binding Sites List in 6s41
Fluorine binding site 2 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:61.4
occ:1.00
F26 A:KUB701 0.0 61.4 1.0
C25 A:KUB701 1.3 55.0 1.0
C24 A:KUB701 2.4 54.4 1.0
C19 A:KUB701 2.4 58.5 1.0
N15 A:KUB701 2.8 57.3 1.0
C16 A:KUB701 2.9 54.5 1.0
CE A:MET243 3.2 56.8 1.0
C18 A:KUB701 3.3 54.6 1.0
C14 A:KUB701 3.6 54.0 1.0
C23 A:KUB701 3.6 56.8 1.0
C20 A:KUB701 3.7 60.3 1.0
C21 A:KUB701 4.1 60.5 1.0
SD A:MET243 4.1 54.4 1.0
C12 A:KUB701 4.3 57.9 1.0
CG A:TYR306 4.3 27.6 1.0
CL1 A:KUB701 4.3 60.8 1.0
CG2 A:VAL211 4.4 31.8 1.0
C27 A:KUB701 4.4 48.7 1.0
CB A:TYR306 4.4 26.8 1.0
CD2 A:TYR306 4.4 31.3 1.0
CG1 A:VAL211 4.5 35.6 1.0
CE3 A:TRP299 4.8 26.9 1.0
CD1 A:TYR306 4.8 29.4 1.0
CZ3 A:TRP299 4.8 26.6 1.0
CE2 A:TYR306 5.0 32.1 1.0

Fluorine binding site 3 out of 6 in 6s41

Go back to Fluorine Binding Sites List in 6s41
Fluorine binding site 3 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:57.9
occ:1.00
F29 A:KUB701 0.0 57.9 1.0
C28 A:KUB701 1.3 51.8 1.0
C27 A:KUB701 2.4 48.7 1.0
C10 A:KUB701 2.4 51.4 1.0
O3 A:KUB701 2.7 50.3 1.0
S2 A:KUB701 3.0 51.3 1.0
CE1 A:HIS407 3.0 36.5 1.0
NE2 A:GLN285 3.4 36.0 1.0
CE A:MET323 3.4 55.1 1.0
CE1 A:PHE281 3.4 23.7 1.0
NE2 A:HIS407 3.5 35.0 1.0
N4 A:KUB701 3.6 56.0 1.0
C11 A:KUB701 3.6 54.6 1.0
C14 A:KUB701 3.7 54.0 1.0
ND1 A:HIS407 3.8 38.1 1.0
CD1 A:PHE281 4.0 24.1 1.0
C12 A:KUB701 4.1 57.9 1.0
O1 A:KUB701 4.3 57.1 1.0
CD A:GLN285 4.4 31.1 1.0
C5 A:KUB701 4.4 65.1 1.0
CD2 A:HIS407 4.5 36.0 1.0
CZ A:PHE281 4.5 24.8 1.0
CG A:HIS407 4.6 35.0 1.0
SD A:MET323 4.7 52.0 1.0
OE1 A:GLN285 4.8 31.7 1.0
N9 A:KUB701 4.9 59.4 1.0
N15 A:KUB701 4.9 57.3 1.0

Fluorine binding site 4 out of 6 in 6s41

Go back to Fluorine Binding Sites List in 6s41
Fluorine binding site 4 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:82.6
occ:1.00
F22 B:KUB701 0.0 82.6 1.0
C21 B:KUB701 1.4 69.7 1.0
C20 B:KUB701 2.4 62.0 1.0
C23 B:KUB701 2.4 65.0 1.0
CZ2 B:TRP299 3.5 18.6 1.0
CD2 B:HIS327 3.5 21.5 1.0
CE B:MET323 3.6 45.1 1.0
CG B:MET323 3.6 35.0 1.0
CD2 B:LEU324 3.6 35.5 1.0
CH2 B:TRP299 3.6 18.9 1.0
C24 B:KUB701 3.6 59.5 1.0
C19 B:KUB701 3.7 57.7 1.0
NE2 B:HIS327 4.0 21.4 1.0
O B:MET323 4.0 24.7 1.0
SD B:MET323 4.1 44.2 1.0
C25 B:KUB701 4.1 59.6 1.0
C B:MET323 4.2 25.0 1.0
CB B:MET323 4.3 29.7 1.0
CD2 B:LEU209 4.4 36.9 1.0
N B:LEU324 4.4 24.2 1.0
OE1 B:GLN285 4.5 24.9 1.0
CE2 B:TRP299 4.5 18.1 1.0
CG B:HIS327 4.5 20.9 1.0
CA B:LEU324 4.6 24.1 1.0
CG B:LEU324 4.6 31.6 1.0
CZ3 B:TRP299 4.7 19.3 1.0
C16 B:KUB701 4.9 59.6 1.0
CA B:MET323 4.9 26.3 1.0

Fluorine binding site 5 out of 6 in 6s41

Go back to Fluorine Binding Sites List in 6s41
Fluorine binding site 5 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:66.8
occ:1.00
F26 B:KUB701 0.0 66.8 1.0
C25 B:KUB701 1.3 59.6 1.0
C24 B:KUB701 2.4 59.5 1.0
C19 B:KUB701 2.4 57.7 1.0
N15 B:KUB701 2.7 63.6 1.0
C16 B:KUB701 2.9 59.6 1.0
C18 B:KUB701 3.4 59.7 1.0
C23 B:KUB701 3.6 65.0 1.0
C14 B:KUB701 3.6 74.1 1.0
C20 B:KUB701 3.7 62.0 1.0
SD B:MET243 3.7 48.5 1.0
C21 B:KUB701 4.1 69.7 1.0
CE B:MET243 4.2 41.7 1.0
CG2 B:VAL211 4.2 29.6 1.0
C27 B:KUB701 4.2 71.1 1.0
CG1 B:VAL211 4.3 29.7 1.0
C12 B:KUB701 4.5 83.5 1.0
CB B:TYR306 4.7 28.5 1.0
CZ3 B:TRP299 4.7 19.3 1.0
CE3 B:TRP299 4.7 19.0 1.0
CL1 B:KUB701 4.8 86.8 1.0
CG B:TYR306 4.8 30.0 1.0
CB B:VAL211 4.9 28.9 1.0
O B:LEU209 5.0 33.8 1.0

Fluorine binding site 6 out of 6 in 6s41

Go back to Fluorine Binding Sites List in 6s41
Fluorine binding site 6 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:58.5
occ:1.00
F29 B:KUB701 0.0 58.5 1.0
C28 B:KUB701 1.3 74.3 1.0
C27 B:KUB701 2.4 71.1 1.0
C10 B:KUB701 2.4 84.2 1.0
O3 B:KUB701 2.7 81.7 1.0
S2 B:KUB701 2.9 81.6 1.0
NE2 B:HIS407 3.2 45.4 1.0
CE B:MET323 3.4 45.1 1.0
CE1 B:PHE281 3.4 19.1 1.0
N4 B:KUB701 3.5 88.5 1.0
C11 B:KUB701 3.6 83.4 1.0
C14 B:KUB701 3.7 74.1 1.0
NE2 B:GLN285 3.7 28.4 1.0
CD2 B:HIS407 3.8 39.9 1.0
CD1 B:PHE281 4.0 22.0 1.0
CE1 B:HIS407 4.1 46.2 1.0
C5 B:KUB701 4.1 90.1 1.0
C12 B:KUB701 4.1 83.5 1.0
N9 B:KUB701 4.2 90.1 1.0
O1 B:KUB701 4.3 93.5 1.0
SD B:MET323 4.5 44.2 1.0
CZ B:PHE281 4.5 20.4 1.0
CD B:GLN285 4.7 25.7 1.0
CG B:HIS407 4.8 38.4 1.0
N15 B:KUB701 4.8 63.6 1.0
ND1 B:HIS407 4.9 45.2 1.0

Reference:

T.Focken, K.Burford, M.E.Grimwood, A.Zenova, J.C.Andrez, W.Gong, M.Wilson, M.Taron, S.Decker, V.Lofstrand, S.Chowdhury, N.Shuart, S.Lin, S.J.Goodchild, C.Young, M.Soriano, P.K.Tari, M.Waldbrook, K.Nelkenbrecher, R.Kwan, A.Lindgren, G.De Boer, S.Lee, L.Sojo, R.J.Devita, C.J.Cohen, S.S.Wesolowski, J.P.Johnson Jr., C.M.Dehnhardt, J.R.Empfield. Identification of Cns-Penetrant Aryl Sulfonamides As Isoform-Selective NAV1.6 Inhibitors with Efficacy in Mouse Models of Epilepsy. J.Med.Chem. V. 62 9618 2019.
ISSN: ISSN 0022-2623
PubMed: 31525968
DOI: 10.1021/ACS.JMEDCHEM.9B01032
Page generated: Tue Jul 15 15:37:01 2025

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