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Fluorine in PDB 8cza: Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075

Protein crystallography data

The structure of Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075, PDB code: 8cza was solved by A.Chan, E.Schonbrunn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.40 / 2.96
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 94.801, 175.737, 143.071, 90, 90, 90
R / Rfree (%) 20.4 / 26.8

Other elements in 8cza:

The structure of Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 (pdb code 8cza). 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 First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075, PDB code: 8cza:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8cza

Go back to Fluorine Binding Sites List in 8cza
Fluorine binding site 1 out of 6 in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075


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 First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:68.3
occ:1.00
F01 B:ZN1201 0.0 68.3 1.0
C16 B:ZN1201 1.4 62.0 1.0
H76 B:ZN1201 2.0 77.4 1.0
C15 B:ZN1201 2.4 67.5 1.0
C17 B:ZN1201 2.4 57.7 1.0
H29 B:ZN1201 2.6 69.2 1.0
N06 B:ZN1201 2.7 64.5 1.0
C22 B:ZN1201 2.9 66.8 1.0
C14 B:ZN1201 3.6 69.3 1.0
C12 B:ZN1201 3.7 46.4 1.0
O02 B:ZN1201 3.8 75.1 1.0
H47 B:ZN1201 3.8 72.1 1.0
C23 B:ZN1201 4.0 64.4 1.0
O03 B:ZN1201 4.0 67.0 1.0
C13 B:ZN1201 4.2 60.5 1.0
H36 B:ZN1201 4.3 98.6 1.0
HG22 B:ILE115 4.4 62.5 1.0
H40 B:ZN1201 4.4 75.7 1.0
HB3 B:ASP113 4.5 71.5 1.0
HD21 B:ASN109 4.5 62.3 1.0
C27 B:ZN1201 4.5 60.0 1.0
H28 B:ZN1201 4.5 83.2 1.0
H39 B:ZN1201 4.7 77.3 1.0
OD1 B:ASP113 4.7 67.8 1.0
HD22 B:ASN109 4.7 62.3 1.0
C24 B:ZN1201 4.8 63.1 1.0
N04 B:ZN1201 4.9 48.5 1.0
H45 B:ZN1201 4.9 68.5 1.0
ND2 B:ASN109 4.9 51.9 1.0
CG B:ASP113 4.9 68.3 1.0
O01 B:ZN1201 4.9 74.0 1.0
HG21 B:ILE115 5.0 62.5 1.0
S01 B:ZN1201 5.0 53.6 1.0

Fluorine binding site 2 out of 6 in 8cza

Go back to Fluorine Binding Sites List in 8cza
Fluorine binding site 2 out of 6 in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075


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 First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:82.5
occ:1.00
F02 B:ZN1201 0.0 82.5 1.0
C49 B:ZN1201 1.4 64.5 1.0
H81 B:ZN1201 1.9 108.0 1.0
HB3 A:LEU61 2.4 106.5 1.0
HD22 A:LEU61 2.4 97.1 1.0
C48 B:ZN1201 2.4 61.0 1.0
C50 B:ZN1201 2.4 68.0 1.0
N14 B:ZN1201 2.5 90.0 1.0
H59 B:ZN1201 2.6 81.7 1.0
C51 B:ZN1201 2.8 82.5 1.0
H11 B:ZN1201 2.8 83.5 1.0
HD11 A:LEU63 3.2 86.2 1.0
CD2 A:LEU61 3.2 80.9 1.0
CB A:LEU61 3.2 88.7 1.0
O A:LEU61 3.2 80.9 1.0
HD23 A:LEU61 3.3 97.1 1.0
HD21 A:LEU63 3.4 98.8 1.0
H64 B:ZN1201 3.4 110.1 1.0
HD13 A:LEU61 3.6 86.1 1.0
C47 B:ZN1201 3.6 76.2 1.0
CG A:LEU61 3.6 87.5 1.0
C45 B:ZN1201 3.6 64.6 1.0
H20 B:ZN1201 3.6 110.5 1.0
C39 B:ZN1201 3.7 69.6 1.0
HA A:LEU61 3.7 110.6 1.0
H9 B:ZN1201 3.8 83.5 1.0
C52 B:ZN1201 3.8 98.5 1.0
HG A:LEU63 3.9 107.6 1.0
CA A:LEU61 3.9 92.2 1.0
H78 B:ZN1201 3.9 73.1 1.0
O08 B:ZN1201 3.9 87.7 1.0
HB2 A:LEU61 3.9 106.5 1.0
HD21 A:LEU61 3.9 97.1 1.0
C A:LEU61 4.0 90.9 1.0
CD1 A:LEU63 4.0 71.8 1.0
C46 B:ZN1201 4.1 71.7 1.0
H10 B:ZN1201 4.1 83.5 1.0
C56 B:ZN1201 4.1 91.7 1.0
CD1 A:LEU61 4.1 71.7 1.0
CD2 A:LEU63 4.2 82.3 1.0
N09 B:ZN1201 4.2 60.9 1.0
CG A:LEU63 4.2 89.6 1.0
C53 B:ZN1201 4.3 92.0 1.0
HD12 A:LEU63 4.5 86.2 1.0
C34 B:ZN1201 4.5 71.6 1.0
H58 B:ZN1201 4.5 91.4 1.0
H14 B:ZN1201 4.5 79.6 1.0
HG A:LEU61 4.5 105.0 1.0
H48 B:ZN1201 4.6 89.2 1.0
HD13 A:LEU63 4.6 86.2 1.0
H60 B:ZN1201 4.7 118.2 1.0
H63 B:ZN1201 4.7 110.1 1.0
H21 B:ZN1201 4.7 110.5 1.0
C33 B:ZN1201 4.7 74.3 1.0
HD11 A:LEU61 4.7 86.1 1.0
HD23 A:LEU63 4.8 98.8 1.0
HD12 A:LEU61 4.8 86.1 1.0
HD22 A:LEU63 4.8 98.8 1.0
C36 B:ZN1201 4.9 60.1 1.0
N13 B:ZN1201 4.9 60.7 1.0
N11 B:ZN1201 5.0 61.1 1.0

Fluorine binding site 3 out of 6 in 8cza

Go back to Fluorine Binding Sites List in 8cza
Fluorine binding site 3 out of 6 in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075


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 First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:54.8
occ:1.00
F01 C:ZN1201 0.0 54.8 1.0
C16 C:ZN1201 1.4 62.7 1.0
H76 C:ZN1201 2.0 73.0 1.0
C15 C:ZN1201 2.4 67.9 1.0
C17 C:ZN1201 2.4 61.9 1.0
H29 C:ZN1201 2.6 74.3 1.0
N06 C:ZN1201 2.7 60.8 1.0
C22 C:ZN1201 2.9 69.3 1.0
C14 C:ZN1201 3.7 65.9 1.0
C12 C:ZN1201 3.7 60.1 1.0
OD1 D:ASP113 3.8 78.5 1.0
OD2 D:ASP113 3.9 50.8 1.0
H47 C:ZN1201 3.9 60.9 1.0
CG D:ASP113 3.9 70.8 1.0
O03 C:ZN1201 4.0 71.8 1.0
C23 C:ZN1201 4.1 54.7 1.0
C13 C:ZN1201 4.1 60.5 1.0
H40 C:ZN1201 4.2 66.4 1.0
HG22 D:ILE115 4.3 86.4 1.0
HB3 D:ASP113 4.3 75.6 1.0
O01 C:ZN1201 4.4 73.8 1.0
C27 C:ZN1201 4.4 50.7 1.0
H28 C:ZN1201 4.5 79.2 1.0
HD21 D:LEU63 4.6 74.6 1.0
HD21 D:ASN109 4.6 67.1 1.0
HD22 D:ASN109 4.6 67.1 1.0
HG21 D:ILE115 4.6 86.4 1.0
H75 C:ZN1201 4.6 73.6 1.0
H46 C:ZN1201 4.7 60.9 1.0
CB D:ASP113 4.7 63.0 1.0
C24 C:ZN1201 4.7 55.3 1.0
H39 C:ZN1201 4.8 65.7 1.0
OD2 D:ASP114 4.8 99.2 1.0
N04 C:ZN1201 4.9 61.7 1.0
ND2 D:ASN109 4.9 55.9 1.0
CG2 D:ILE115 4.9 72.0 1.0
H43 C:ZN1201 4.9 73.6 1.0

Fluorine binding site 4 out of 6 in 8cza

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Fluorine binding site 4 out of 6 in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075


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 First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:85.6
occ:1.00
F02 C:ZN1201 0.0 85.6 1.0
C49 C:ZN1201 1.4 72.0 1.0
H20 C:ZN1201 2.3 108.4 1.0
H60 C:ZN1201 2.3 108.5 1.0
C50 C:ZN1201 2.4 63.4 1.0
C48 C:ZN1201 2.4 73.2 1.0
H59 C:ZN1201 2.6 76.2 1.0
H78 C:ZN1201 2.7 92.0 1.0
C52 C:ZN1201 3.0 90.4 1.0
HB3 C:LEU61 3.0 104.6 1.0
N09 C:ZN1201 3.0 76.6 1.0
C53 C:ZN1201 3.1 90.3 1.0
HG C:LEU61 3.1 105.3 1.0
C51 C:ZN1201 3.1 75.8 1.0
N14 C:ZN1201 3.3 81.5 1.0
HD23 C:LEU61 3.4 105.3 1.0
C34 C:ZN1201 3.6 65.3 1.0
H21 C:ZN1201 3.6 108.4 1.0
C45 C:ZN1201 3.6 57.1 1.0
C47 C:ZN1201 3.7 74.5 1.0
CG C:LEU61 3.7 87.8 1.0
CB C:LEU61 3.7 87.1 1.0
O06 C:ZN1201 3.8 76.1 1.0
S02 C:ZN1201 3.8 59.9 1.0
O07 C:ZN1201 4.0 79.3 1.0
CD2 C:LEU61 4.0 87.8 1.0
O C:LEU61 4.0 88.7 1.0
H48 C:ZN1201 4.0 77.9 1.0
C33 C:ZN1201 4.1 64.9 1.0
H61 C:ZN1201 4.1 115.0 1.0
C46 C:ZN1201 4.1 66.7 1.0
HD22 C:LEU63 4.2 117.7 1.0
HA C:LEU61 4.2 114.2 1.0
C54 C:ZN1201 4.2 95.8 1.0
O08 C:ZN1201 4.2 79.2 1.0
C35 C:ZN1201 4.3 74.0 1.0
H81 C:ZN1201 4.3 97.8 1.0
C56 C:ZN1201 4.3 91.0 1.0
HD13 C:LEU63 4.4 79.5 1.0
HD21 C:LEU61 4.4 105.3 1.0
CA C:LEU61 4.4 95.1 1.0
H49 C:ZN1201 4.4 88.9 1.0
HB2 C:LEU61 4.5 104.6 1.0
HG3 D:LYS60 4.5 88.2 1.0
H64 C:ZN1201 4.5 109.3 1.0
H58 C:ZN1201 4.6 89.5 1.0
C C:LEU61 4.7 94.1 1.0
HD21 C:LEU63 4.7 117.7 1.0
H62 C:ZN1201 4.8 115.0 1.0
HD22 C:LEU61 4.8 105.3 1.0
CD2 C:LEU63 4.9 98.1 1.0
N11 C:ZN1201 4.9 51.1 1.0
N13 C:ZN1201 4.9 48.8 1.0
HD2 D:LYS60 5.0 90.8 1.0
H63 C:ZN1201 5.0 109.3 1.0

Fluorine binding site 5 out of 6 in 8cza

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Fluorine binding site 5 out of 6 in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075


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 First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:67.2
occ:1.00
F01 F:ZN1201 0.0 67.2 1.0
C16 F:ZN1201 1.4 53.5 1.0
H76 F:ZN1201 1.8 58.6 1.0
C17 F:ZN1201 2.4 52.7 1.0
C15 F:ZN1201 2.4 62.0 1.0
N06 F:ZN1201 2.6 48.8 1.0
H29 F:ZN1201 2.6 63.3 1.0
C22 F:ZN1201 2.9 64.0 1.0
C12 F:ZN1201 3.7 52.1 1.0
C14 F:ZN1201 3.7 60.2 1.0
H40 F:ZN1201 3.8 65.4 1.0
C23 F:ZN1201 3.9 58.3 1.0
OD1 F:ASP113 4.0 56.7 1.0
O03 F:ZN1201 4.0 66.3 1.0
C13 F:ZN1201 4.1 58.1 1.0
H47 F:ZN1201 4.2 78.9 1.0
HG22 F:ILE115 4.3 68.7 1.0
O02 F:ZN1201 4.3 56.4 1.0
C24 F:ZN1201 4.4 54.5 1.0
HB3 F:ASP113 4.5 80.1 1.0
CG F:ASP113 4.5 67.9 1.0
C27 F:ZN1201 4.5 65.7 1.0
H28 F:ZN1201 4.5 72.2 1.0
HD21 F:LEU63 4.5 70.5 1.0
H46 F:ZN1201 4.6 78.9 1.0
H39 F:ZN1201 4.6 70.0 1.0
O01 F:ZN1201 4.7 71.7 1.0
H41 F:ZN1201 4.7 65.4 1.0
HG21 F:ILE115 4.8 68.7 1.0
N04 F:ZN1201 4.8 48.5 1.0
OD1 F:ASN109 4.9 45.1 1.0
H74 F:ZN1201 5.0 58.2 1.0

Fluorine binding site 6 out of 6 in 8cza

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Fluorine binding site 6 out of 6 in the Crystal Structure of the First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075


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 First Bromodomain (BD1) of Human Brdt Bound to Gxh-IV-075 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:84.1
occ:1.00
F02 F:ZN1201 0.0 84.1 1.0
C49 F:ZN1201 1.4 82.3 1.0
C48 F:ZN1201 2.4 78.2 1.0
C50 F:ZN1201 2.4 62.2 1.0
HZ2 F:LYS60 2.4 81.4 1.0
O08 F:ZN1201 2.5 81.7 1.0
H59 F:ZN1201 2.6 74.7 1.0
C51 F:ZN1201 2.8 76.8 1.0
HZ3 F:LYS60 2.9 81.4 1.0
NZ F:LYS60 3.0 67.8 1.0
HZ1 F:LYS60 3.3 81.4 1.0
C47 F:ZN1201 3.7 69.0 1.0
C45 F:ZN1201 3.7 63.8 1.0
HG3 F:LYS60 3.9 86.2 1.0
C46 F:ZN1201 4.1 66.3 1.0
O06 F:ZN1201 4.2 64.6 1.0
N14 F:ZN1201 4.2 77.8 1.0
HD11 E:LEU63 4.3 92.6 1.0
CE F:LYS60 4.4 68.7 1.0
HD3 F:LYS60 4.4 89.3 1.0
H58 F:ZN1201 4.5 82.8 1.0
HD21 E:ASN109 4.6 85.6 1.0
CD F:LYS60 4.7 74.4 1.0
CG F:LYS60 4.7 71.8 1.0
H60 F:ZN1201 4.7 99.1 1.0
HE3 F:LYS60 4.7 82.5 1.0
H81 F:ZN1201 4.8 93.4 1.0
N13 F:ZN1201 4.9 65.0 1.0
H80 F:ZN1201 5.0 78.0 1.0
HG2 F:LYS60 5.0 86.2 1.0

Reference:

X.Guan, N.Cheryala, R.M.Karim, A.Chan, N.Berndt, J.Qi, G.I.Georg, E.Schonbrunn. Bivalent Bet Bromodomain Inhibitors Confer Increased Potency and Selectivity For Brdt Via Protein Conformational Plasticity. J.Med.Chem. V. 65 10441 2022.
ISSN: ISSN 0022-2623
PubMed: 35867655
DOI: 10.1021/ACS.JMEDCHEM.2C00453
Page generated: Wed Jul 16 03:15:26 2025

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