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Fluorine in PDB 5kcw: Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative

Protein crystallography data

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative, PDB code: 5kcw was solved by J.C.Nwachukwu, S.Srinivasan, N.E.Bruno, V.Dharmarajan, D.Goswami, I.Kastrati, S.Novick, J.Nowak, H.B.Zhou, N.Boonmuen, Y.Zhao, J.Min, J.Frasor, B.S.Katzenellenbogen, P.R.Griffin, J.A.Katzenellenbogen, K.W.Nettles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.80 / 1.91
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.627, 81.529, 58.976, 90.00, 110.93, 90.00
R / Rfree (%) 19 / 24.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative (pdb code 5kcw). 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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative, PDB code: 5kcw:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5kcw

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Fluorine binding site 1 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative


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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:55.4
occ:0.32
 F01 B:OB9601 0.0 55.4 0.3
C21 B:OB9602 0.6 60.3 0.7
C22 B:OB9602 1.0 55.6 0.7
C26 B:OB9601 1.3 56.2 0.3
C19 B:OB9602 1.8 56.8 0.7
F03 B:OB9601 2.0 49.8 0.3
F02 B:OB9601 2.0 56.5 0.3
C23 B:OB9602 2.1 57.4 0.7
C20 B:OB9601 2.3 54.7 0.3
C25 B:OB9602 2.5 54.6 0.7
C24 B:OB9602 2.6 57.7 0.7
N01 B:OB9602 2.8 54.5 0.7
N01 B:OB9601 2.9 53.4 0.3
C21 B:OB9601 3.2 64.5 0.3
C19 B:OB9601 3.4 61.4 0.3
C20 B:OB9602 3.4 63.8 0.7
C03 B:OB9602 3.7 41.7 0.7
C03 B:OB9601 3.7 40.9 0.3
C02 B:OB9602 3.7 41.0 0.7
C02 B:OB9601 3.7 41.0 0.3
C01 B:OB9602 3.8 40.9 0.7
C01 B:OB9601 3.9 40.6 0.3
C04 B:OB9602 3.9 41.1 0.7
C04 B:OB9601 3.9 40.3 0.3
F02 B:OB9602 3.9 67.8 0.7
CD2 B:LEU525 3.9 61.7 1.0
C06 B:OB9602 4.0 37.8 0.7
C06 B:OB9601 4.0 38.2 0.3
C05 B:OB9602 4.0 37.1 0.7
C05 B:OB9601 4.0 37.9 0.3
S01 B:OB9601 4.1 47.9 0.3
S01 B:OB9602 4.2 45.8 0.7
C17 B:OB9601 4.3 39.3 0.3
C26 B:OB9602 4.3 65.8 0.7
O01 B:OB9602 4.3 42.4 0.7
O01 B:OB9601 4.3 41.6 0.3
C17 B:OB9602 4.3 39.3 0.7
C22 B:OB9601 4.3 62.8 0.3
CD1 B:LEU525 4.4 61.0 1.0
C11 B:OB9601 4.6 38.0 0.3
C11 B:OB9602 4.6 36.0 0.7
CG B:LEU525 4.6 58.7 1.0
O05 B:OB9602 4.6 49.9 0.7
C25 B:OB9601 4.7 65.4 0.3
C07 B:OB9601 4.7 38.3 0.3
C07 B:OB9602 4.7 36.2 0.7
O05 B:OB9601 4.7 52.5 0.3
CB B:LEU525 4.8 61.9 1.0

Fluorine binding site 2 out of 6 in 5kcw

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Fluorine binding site 2 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative


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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:56.5
occ:0.32
 F02 B:OB9601 0.0 56.5 0.3
C23 B:OB9602 0.3 57.4 0.7
C24 B:OB9602 1.1 57.7 0.7
C26 B:OB9601 1.3 56.2 0.3
C22 B:OB9602 1.3 55.6 0.7
F01 B:OB9601 2.0 55.4 0.3
C25 B:OB9602 2.1 54.6 0.7
F03 B:OB9601 2.1 49.8 0.3
C21 B:OB9602 2.2 60.3 0.7
C20 B:OB9601 2.3 54.7 0.3
C19 B:OB9602 2.5 56.8 0.7
CD2 B:LEU525 3.6 61.7 1.0
N01 B:OB9601 3.7 53.4 0.3
N01 B:OB9602 3.8 54.5 0.7
CD2 B:LEU544 4.1 84.7 1.0
CH2 B:TRP383 4.2 42.0 1.0
CD2 B:LEU384 4.2 33.0 1.0
C19 B:OB9601 4.4 61.4 0.3
CB B:LEU525 4.5 61.9 1.0
CG B:LEU525 4.6 58.7 1.0
C21 B:OB9601 4.6 64.5 0.3
O05 B:OB9602 4.6 49.9 0.7
CZ2 B:TRP383 4.7 52.2 1.0
O B:GLY521 4.7 50.5 1.0
S01 B:OB9601 4.7 47.9 0.3
O05 B:OB9601 4.7 52.5 0.3
F02 B:OB9602 4.8 67.8 0.7
SD B:MET522 4.8 70.0 1.0
S01 B:OB9602 4.8 45.8 0.7
C20 B:OB9602 4.8 63.8 0.7
C B:GLY521 4.8 49.8 1.0
CD1 B:LEU384 4.9 36.2 1.0
C01 B:OB9602 4.9 40.9 0.7
C01 B:OB9601 4.9 40.6 0.3
CG B:LEU544 4.9 84.3 1.0
N B:MET522 4.9 46.7 1.0
C06 B:OB9602 5.0 37.8 0.7
C06 B:OB9601 5.0 38.2 0.3
CA B:MET522 5.0 44.4 1.0
C17 B:OB9601 5.0 39.3 0.3

Fluorine binding site 3 out of 6 in 5kcw

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Fluorine binding site 3 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative


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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:49.8
occ:0.32
 F03 B:OB9601 0.0 49.8 0.3
C26 B:OB9601 1.3 56.2 0.3
C21 B:OB9602 1.6 60.3 0.7
C22 B:OB9602 1.8 55.6 0.7
F01 B:OB9601 2.0 55.4 0.3
C19 B:OB9602 2.0 56.8 0.7
F02 B:OB9601 2.1 56.5 0.3
C23 B:OB9602 2.2 57.4 0.7
C20 B:OB9601 2.3 54.7 0.3
C25 B:OB9602 2.4 54.6 0.7
C24 B:OB9602 2.5 57.7 0.7
N01 B:OB9602 2.9 54.5 0.7
N01 B:OB9601 3.0 53.4 0.3
C17 B:OB9601 3.1 39.3 0.3
C17 B:OB9602 3.2 39.3 0.7
C06 B:OB9602 3.3 37.8 0.7
C06 B:OB9601 3.3 38.2 0.3
S01 B:OB9601 3.5 47.9 0.3
S01 B:OB9602 3.5 45.8 0.7
O05 B:OB9602 3.5 49.9 0.7
C05 B:OB9602 3.6 37.1 0.7
C05 B:OB9601 3.6 37.9 0.3
O05 B:OB9601 3.6 52.5 0.3
C01 B:OB9602 3.6 40.9 0.7
C01 B:OB9601 3.6 40.6 0.3
CD1 B:LEU384 3.7 36.2 1.0
C07 B:OB9602 3.9 36.2 0.7
C07 B:OB9601 3.9 38.3 0.3
C11 B:OB9601 3.9 38.0 0.3
C11 B:OB9602 3.9 36.0 0.7
CD2 B:LEU384 4.0 33.0 1.0
C19 B:OB9601 4.0 61.4 0.3
C04 B:OB9602 4.1 41.1 0.7
C04 B:OB9601 4.1 40.3 0.3
C20 B:OB9602 4.1 63.8 0.7
C02 B:OB9602 4.2 41.0 0.7
C02 B:OB9601 4.2 41.0 0.3
C18 B:OB9601 4.3 35.4 0.3
C03 B:OB9602 4.4 41.7 0.7
C03 B:OB9601 4.4 40.9 0.3
C18 B:OB9602 4.4 34.8 0.7
C21 B:OB9601 4.4 64.5 0.3
CH2 B:TRP383 4.5 42.0 1.0
CG B:LEU384 4.5 38.6 1.0
C08 B:OB9602 4.7 39.4 0.7
O04 B:OB9601 4.7 46.0 0.3
C08 B:OB9601 4.7 39.5 0.3
O04 B:OB9602 4.8 45.3 0.7
CZ3 B:TRP383 4.9 39.3 1.0

Fluorine binding site 4 out of 6 in 5kcw

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Fluorine binding site 4 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative


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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:61.8
occ:0.68
 F01 B:OB9602 0.0 61.8 0.7
C23 B:OB9601 0.4 63.0 0.3
C22 B:OB9601 1.1 62.8 0.3
C26 B:OB9602 1.3 65.8 0.7
C24 B:OB9601 1.3 64.7 0.3
C21 B:OB9601 2.0 64.5 0.3
F02 B:OB9602 2.0 67.8 0.7
F03 B:OB9602 2.0 65.0 0.7
C25 B:OB9601 2.1 65.4 0.3
C20 B:OB9602 2.3 63.8 0.7
C19 B:OB9601 2.4 61.4 0.3
CG B:MET421 3.4 76.3 1.0
N01 B:OB9602 3.6 54.5 0.7
N01 B:OB9601 3.7 53.4 0.3
SD B:MET421 3.9 0.4 1.0
C19 B:OB9602 4.4 56.8 0.7
O04 B:OB9601 4.5 46.0 0.3
O04 B:OB9602 4.5 45.3 0.7
S01 B:OB9602 4.6 45.8 0.7
CE B:MET343 4.6 63.3 1.0
S01 B:OB9601 4.6 47.9 0.3
CB B:HIS524 4.6 80.1 1.0
C20 B:OB9601 4.7 54.7 0.3
CB B:MET421 4.7 69.8 1.0
O B:HIS524 4.8 80.9 1.0
C B:HIS524 4.8 67.4 1.0
CA B:MET421 4.8 64.7 1.0
N B:MET421 4.8 74.7 1.0
N B:LEU525 4.9 64.2 1.0
CA B:LEU525 4.9 65.9 1.0

Fluorine binding site 5 out of 6 in 5kcw

Go back to Fluorine Binding Sites List in 5kcw
Fluorine binding site 5 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative


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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:67.8
occ:0.68
 F02 B:OB9602 0.0 67.8 0.7
C26 B:OB9602 1.3 65.8 0.7
C21 B:OB9601 1.5 64.5 0.3
C22 B:OB9601 1.7 62.8 0.3
C19 B:OB9601 1.8 61.4 0.3
F01 B:OB9602 2.0 61.8 0.7
C25 B:OB9601 2.0 65.4 0.3
C23 B:OB9601 2.0 63.0 0.3
F03 B:OB9602 2.1 65.0 0.7
C24 B:OB9601 2.2 64.7 0.3
C20 B:OB9602 2.2 63.8 0.7
N01 B:OB9601 2.8 53.4 0.3
N01 B:OB9602 2.9 54.5 0.7
C19 B:OB9602 3.1 56.8 0.7
C20 B:OB9601 3.2 54.7 0.3
CA B:LEU525 3.4 65.9 1.0
C25 B:OB9602 3.4 54.6 0.7
N B:LEU525 3.5 64.2 1.0
CB B:LEU525 3.5 61.9 1.0
O B:GLY521 3.7 50.5 1.0
CD1 B:LEU525 3.8 61.0 1.0
C21 B:OB9602 3.8 60.3 0.7
F01 B:OB9601 3.9 55.4 0.3
C B:HIS524 3.9 67.4 1.0
C26 B:OB9601 4.1 56.2 0.3
S01 B:OB9602 4.2 45.8 0.7
S01 B:OB9601 4.2 47.9 0.3
CG B:LEU525 4.2 58.7 1.0
O B:HIS524 4.3 80.9 1.0
CB B:HIS524 4.3 80.1 1.0
C24 B:OB9602 4.3 57.7 0.7
O04 B:OB9601 4.6 46.0 0.3
C22 B:OB9602 4.7 55.6 0.7
CA B:HIS524 4.7 71.6 1.0
O04 B:OB9602 4.7 45.3 0.7
C B:GLY521 4.7 49.8 1.0
F02 B:OB9601 4.8 56.5 0.3
CD2 B:LEU525 4.8 61.7 1.0
O05 B:OB9602 4.9 49.9 0.7
C B:LEU525 4.9 69.9 1.0
C23 B:OB9602 4.9 57.4 0.7

Fluorine binding site 6 out of 6 in 5kcw

Go back to Fluorine Binding Sites List in 5kcw
Fluorine binding site 6 out of 6 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative


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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl Obhs-N Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:65.0
occ:0.68
 F03 B:OB9602 0.0 65.0 0.7
C25 B:OB9601 0.5 65.4 0.3
C24 B:OB9601 1.0 64.7 0.3
C26 B:OB9602 1.3 65.8 0.7
C19 B:OB9601 1.7 61.4 0.3
F01 B:OB9602 2.0 61.8 0.7
F02 B:OB9602 2.1 67.8 0.7
C23 B:OB9601 2.1 63.0 0.3
C20 B:OB9602 2.2 63.8 0.7
C21 B:OB9601 2.5 64.5 0.3
N01 B:OB9601 2.6 53.4 0.3
C22 B:OB9601 2.6 62.8 0.3
N01 B:OB9602 2.8 54.5 0.7
O04 B:OB9601 3.3 46.0 0.3
S01 B:OB9602 3.3 45.8 0.7
O04 B:OB9602 3.3 45.3 0.7
S01 B:OB9601 3.3 47.9 0.3
C19 B:OB9602 3.6 56.8 0.7
CB B:HIS524 3.6 80.1 1.0
C20 B:OB9601 3.7 54.7 0.3
O B:GLY521 3.8 50.5 1.0
C25 B:OB9602 4.0 54.6 0.7
O05 B:OB9602 4.0 49.9 0.7
CG B:MET421 4.1 76.3 1.0
O05 B:OB9601 4.1 52.5 0.3
SD B:MET421 4.2 0.4 1.0
CG1 B:ILE424 4.4 57.0 1.0
N B:LEU525 4.5 64.2 1.0
CA B:GLY521 4.5 48.3 1.0
C B:HIS524 4.5 67.4 1.0
C B:GLY521 4.6 49.8 1.0
CG B:HIS524 4.6 89.6 1.0
ND1 B:HIS524 4.6 93.2 1.0
CA B:HIS524 4.7 71.6 1.0
O B:GLY420 4.7 74.6 1.0
CA B:MET421 4.7 64.7 1.0
C21 B:OB9602 4.7 60.3 0.7
C B:GLY420 4.9 76.3 1.0
C26 B:OB9601 4.9 56.2 0.3
O B:HIS524 4.9 80.9 1.0
N B:MET421 5.0 74.7 1.0
C17 B:OB9602 5.0 39.3 0.7
CA B:LEU525 5.0 65.9 1.0
C17 B:OB9601 5.0 39.3 0.3

Reference:

S.Srinivasan, J.C.Nwachukwu, N.E.Bruno, V.Dharmarajan, D.Goswami, I.Kastrati, S.Novick, J.Nowak, V.Cavett, H.B.Zhou, N.Boonmuen, Y.Zhao, J.Min, J.Frasor, B.S.Katzenellenbogen, P.R.Griffin, J.A.Katzenellenbogen, K.W.Nettles. Full Antagonism of the Estrogen Receptor Without A Prototypical Ligand Side Chain. Nat. Chem. Biol. V. 13 111 2017.
ISSN: ESSN 1552-4469
PubMed: 27870835
DOI: 10.1038/NCHEMBIO.2236
Page generated: Tue Jul 15 04:45:09 2025

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