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Fluorine in PDB 5kd9: Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl 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 4-Chlorobenzyl Obhs-N Derivative, PDB code: 5kd9 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) 45.56 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.951, 81.654, 58.795, 90.00, 110.97, 90.00
R / Rfree (%) 18.4 / 21.3

Other elements in 5kd9:

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

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 4-Chlorobenzyl Obhs-N Derivative (pdb code 5kd9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative, PDB code: 5kd9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5kd9

Go back to Fluorine Binding Sites List in 5kd9
Fluorine binding site 1 out of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl 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 4-Chlorobenzyl Obhs-N Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:71.2
occ:1.00
F1 B:OBT601 0.0 71.2 1.0
C20 B:OBT601 1.3 69.1 1.0
F2 B:OBT601 2.0 68.8 1.0
F3 B:OBT601 2.0 71.7 1.0
C19 B:OBT601 2.2 63.7 1.0
N01 B:OBT601 3.0 53.9 1.0
C21 B:OBT601 3.2 46.3 1.0
C22 B:OBT601 3.4 43.7 1.0
C26 B:OBT601 4.0 45.9 1.0
CA B:LEU525 4.1 56.0 1.0
N B:LEU525 4.2 54.8 1.0
C23 B:OBT601 4.3 42.7 1.0
CB B:LEU525 4.3 52.6 1.0
CD1 B:LEU525 4.4 49.5 1.0
CE B:MET343 4.4 53.5 1.0
S01 B:OBT601 4.4 40.7 1.0
O B:GLY521 4.5 39.0 1.0
C B:HIS524 4.5 58.2 1.0
CB B:HIS524 4.7 66.0 1.0
O B:HIS524 4.7 60.0 1.0
C25 B:OBT601 4.8 42.3 1.0
O04 B:OBT601 4.9 35.8 1.0
C24 B:OBT601 4.9 43.5 1.0

Fluorine binding site 2 out of 3 in 5kd9

Go back to Fluorine Binding Sites List in 5kd9
Fluorine binding site 2 out of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl 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 4-Chlorobenzyl Obhs-N Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:68.8
occ:1.00
F2 B:OBT601 0.0 68.8 1.0
C20 B:OBT601 1.3 69.1 1.0
F1 B:OBT601 2.0 71.2 1.0
F3 B:OBT601 2.0 71.7 1.0
C19 B:OBT601 2.3 63.7 1.0
N01 B:OBT601 3.6 53.9 1.0
CB B:HIS524 3.7 66.0 1.0
O B:GLU419 4.1 0.5 1.0
CB B:MET421 4.3 58.6 1.0
N B:MET421 4.3 64.2 1.0
CA B:MET421 4.3 57.0 1.0
C21 B:OBT601 4.4 46.3 1.0
ND1 B:HIS524 4.4 80.0 1.0
O04 B:OBT601 4.4 35.8 1.0
CG B:MET421 4.5 56.6 1.0
CG1 B:VAL418 4.5 0.7 1.0
S01 B:OBT601 4.5 40.7 1.0
C B:HIS524 4.5 58.2 1.0
CG B:HIS524 4.6 74.2 1.0
C B:GLY420 4.7 0.1 1.0
N B:LEU525 4.7 54.8 1.0
O B:HIS524 4.7 60.0 1.0
CA B:HIS524 4.8 59.4 1.0
O B:GLY521 4.8 39.0 1.0
C22 B:OBT601 4.9 43.7 1.0

Fluorine binding site 3 out of 3 in 5kd9

Go back to Fluorine Binding Sites List in 5kd9
Fluorine binding site 3 out of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl 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 4-Chlorobenzyl Obhs-N Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:71.7
occ:1.00
F3 B:OBT601 0.0 71.7 1.0
C20 B:OBT601 1.3 69.1 1.0
F2 B:OBT601 2.0 68.8 1.0
F1 B:OBT601 2.0 71.2 1.0
C19 B:OBT601 2.2 63.7 1.0
N01 B:OBT601 2.6 53.9 1.0
C21 B:OBT601 3.3 46.3 1.0
O04 B:OBT601 3.4 35.8 1.0
S01 B:OBT601 3.4 40.7 1.0
C22 B:OBT601 3.5 43.7 1.0
CG B:MET421 3.6 56.6 1.0
SD B:MET421 3.8 80.5 1.0
CE B:MET343 3.9 53.5 1.0
CB B:MET421 4.0 58.6 1.0
SD B:MET343 4.2 88.6 1.0
C11 B:OBT601 4.3 35.5 1.0
C17 B:OBT601 4.4 33.5 1.0
CG1 B:VAL418 4.5 0.7 1.0
C26 B:OBT601 4.5 45.9 1.0
CA B:MET421 4.6 57.0 1.0
O05 B:OBT601 4.6 45.4 1.0
C23 B:OBT601 4.7 42.7 1.0
O03 B:OBT601 5.0 37.5 1.0

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 04:46:51 2025

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