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Fluorine in PDB 5gmz: Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine

Protein crystallography data

The structure of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine, PDB code: 5gmz was solved by Z.H.Xu, Z.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.31 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 66.017, 67.215, 87.669, 68.10, 68.43, 83.07
R / Rfree (%) 17.4 / 19.6

Other elements in 5gmz:

The structure of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Fluorine atom in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine (pdb code 5gmz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 21 binding sites of Fluorine where determined in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine, PDB code: 5gmz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 21 in 5gmz

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Fluorine binding site 1 out of 21 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F205

b:27.1
occ:1.00
 F22 A:6XU205 0.0 27.1 1.0
C16 A:6XU205 1.3 26.0 1.0
F23 A:6XU205 2.1 27.1 1.0
C15 A:6XU205 2.4 23.2 1.0
C17 A:6XU205 2.5 28.6 1.0
C18 A:6XU205 3.5 30.6 1.0
N14 A:6XU205 3.5 26.7 1.0
C13 A:6XU205 4.7 26.8 1.0
C19 A:6XU205 4.9 32.8 1.0

Fluorine binding site 2 out of 21 in 5gmz

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Fluorine binding site 2 out of 21 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F205

b:27.1
occ:1.00
 F23 A:6XU205 0.0 27.1 1.0
C16 A:6XU205 1.3 26.0 1.0
F22 A:6XU205 2.1 27.1 1.0
C15 A:6XU205 2.3 23.2 1.0
C17 A:6XU205 2.4 28.6 1.0
N14 A:6XU205 3.0 26.7 1.0
C18 A:6XU205 3.4 30.6 1.0
O A:HOH348 3.5 26.6 1.0
N05 A:6XU205 4.1 24.3 1.0
N09 A:6XU205 4.1 26.6 1.0
C13 A:6XU205 4.3 26.8 1.0
C19 A:6XU205 4.4 32.8 1.0
O21 A:6XU205 4.6 31.4 1.0
C04 A:6XU205 4.7 28.6 1.0
C08 A:6XU205 4.8 30.9 1.0
C10 A:6XU205 4.8 26.0 1.0
C06 A:6XU205 4.9 27.1 1.0

Fluorine binding site 3 out of 21 in 5gmz

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Fluorine binding site 3 out of 21 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F205

b:27.0
occ:1.00
 F34 A:6XU205 0.0 27.0 1.0
C31 A:6XU205 1.3 23.8 1.0
C32 A:6XU205 2.3 23.3 1.0
C30 A:6XU205 2.4 27.3 1.0
OG1 A:THR33 3.1 22.8 1.0
O A:ASP29 3.3 20.7 1.0
C33 A:6XU205 3.6 27.2 1.0
C29 A:6XU205 3.6 24.7 1.0
C A:ASP29 3.7 20.5 1.0
CB A:PRO25 3.7 24.2 1.0
CG A:PRO25 3.9 23.5 1.0
CB A:ASP29 3.9 19.5 1.0
CB A:THR33 4.0 24.6 1.0
N A:LEU30 4.1 19.8 1.0
C28 A:6XU205 4.1 26.6 1.0
CA A:LEU30 4.3 20.6 1.0
CA A:ASP29 4.4 22.6 1.0
CD2 A:LEU30 4.4 23.1 1.0
CG2 A:THR33 4.5 24.9 1.0
CG A:LEU30 4.8 20.8 1.0

Fluorine binding site 4 out of 21 in 5gmz

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Fluorine binding site 4 out of 21 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F206

b:93.0
occ:1.00
 F22 A:6XU206 0.0 93.0 1.0
C16 A:6XU206 1.3 88.3 1.0
F23 A:6XU206 2.1 91.2 1.0
C15 A:6XU206 2.4 83.6 1.0
C17 A:6XU206 2.4 84.4 1.0
N14 A:6XU206 3.4 78.4 1.0
O B:HOH408 3.5 64.8 1.0
C18 A:6XU206 3.5 83.6 1.0
C13 A:6XU206 4.0 72.4 1.0
C19 A:6XU206 4.7 84.4 1.0

Fluorine binding site 5 out of 21 in 5gmz

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Fluorine binding site 5 out of 21 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F206

b:91.2
occ:1.00
 F23 A:6XU206 0.0 91.2 1.0
C16 A:6XU206 1.3 88.3 1.0
F22 A:6XU206 2.1 93.0 1.0
C15 A:6XU206 2.4 83.6 1.0
C17 A:6XU206 2.4 84.4 1.0
C18 A:6XU206 3.3 83.6 1.0
N14 A:6XU206 3.4 78.4 1.0
C19 A:6XU206 3.7 84.4 1.0
O21 A:6XU206 4.0 86.1 1.0
O20 A:6XU206 4.3 79.5 1.0
C13 A:6XU206 4.6 72.4 1.0
O A:HOH321 4.6 45.9 1.0
O B:HOH408 4.7 64.8 1.0

Fluorine binding site 6 out of 21 in 5gmz

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Fluorine binding site 6 out of 21 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F206

b:64.4
occ:1.00
 F34 A:6XU206 0.0 64.4 1.0
C31 A:6XU206 1.3 66.0 1.0
C32 A:6XU206 2.3 60.1 1.0
C30 A:6XU206 2.4 66.1 1.0
CG2 B:VAL85 3.5 34.7 1.0
CD1 B:LEU76 3.5 32.9 1.0
C33 A:6XU206 3.6 62.9 1.0
C29 A:6XU206 3.6 62.5 1.0
CD2 B:LEU76 3.9 30.3 1.0
C28 A:6XU206 4.2 64.1 1.0
CG B:LEU76 4.3 33.0 1.0
O B:SER81 4.4 36.6 1.0
CZ3 A:TRP71 4.4 37.0 1.0
CB B:SER81 4.5 39.2 1.0
CB A:ASN75 4.5 38.2 1.0
CH2 A:TRP71 4.6 31.3 1.0
C B:SER81 4.9 33.9 1.0
CG1 A:VAL72 4.9 32.8 1.0
CG1 B:VAL72 4.9 35.2 1.0
CG2 A:VAL72 4.9 32.9 1.0
CA A:VAL72 5.0 29.4 1.0
O A:VAL72 5.0 34.0 1.0
OG B:SER81 5.0 37.6 1.0
CB B:VAL85 5.0 34.3 1.0

Fluorine binding site 7 out of 21 in 5gmz

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Fluorine binding site 7 out of 21 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:27.2
occ:1.00
 F22 B:6XU202 0.0 27.2 1.0
C16 B:6XU202 1.3 24.2 1.0
F23 B:6XU202 2.1 26.6 1.0
C15 B:6XU202 2.3 19.3 1.0
C17 B:6XU202 2.4 30.8 1.0
CD1 C:TRP125 3.0 27.7 1.0
CA C:TRP125 3.4 25.2 1.0
C18 B:6XU202 3.4 28.3 1.0
N14 B:6XU202 3.5 23.9 1.0
CD C:PRO134 3.6 30.0 1.0
CB C:TRP125 3.6 22.9 1.0
CG C:TRP125 3.6 27.3 1.0
O C:HOH339 3.9 30.9 1.0
OG1 C:THR128 3.9 25.9 1.0
CB C:ARG133 4.0 28.3 1.0
O C:HOH396 4.1 45.3 1.0
NE1 C:TRP125 4.2 30.2 1.0
CG C:ARG133 4.2 51.9 1.0
O C:TRP125 4.2 24.4 1.0
CB C:THR128 4.3 24.1 1.0
N C:TRP125 4.3 25.2 1.0
C C:TRP125 4.3 21.7 1.0
CG C:PRO134 4.4 32.7 1.0
C13 B:6XU202 4.6 25.1 1.0
CG2 C:THR128 4.6 23.4 1.0
CA C:ARG133 4.7 28.1 1.0
N C:PRO134 4.7 29.2 1.0
O C:VAL124 4.8 25.5 1.0
C19 B:6XU202 4.8 32.5 1.0
C C:VAL124 4.9 26.7 1.0
CD2 C:TRP125 4.9 26.6 1.0

Fluorine binding site 8 out of 21 in 5gmz

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Fluorine binding site 8 out of 21 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:26.6
occ:1.00
 F23 B:6XU202 0.0 26.6 1.0
C16 B:6XU202 1.3 24.2 1.0
F22 B:6XU202 2.1 27.2 1.0
C15 B:6XU202 2.4 19.3 1.0
C17 B:6XU202 2.5 30.8 1.0
N14 B:6XU202 3.0 23.9 1.0
CD C:PRO134 3.3 30.0 1.0
C18 B:6XU202 3.4 28.3 1.0
O B:HOH371 3.4 26.4 1.0
CG2 C:THR128 3.5 23.4 1.0
CB C:ARG133 3.5 28.3 1.0
OG1 C:THR128 3.7 25.9 1.0
CA C:ARG133 3.7 28.1 1.0
O C:HOH331 3.8 32.7 1.0
CB C:THR128 3.9 24.1 1.0
N09 B:6XU202 4.0 24.9 1.0
N05 B:6XU202 4.0 23.8 1.0
N C:PRO134 4.3 29.2 1.0
C13 B:6XU202 4.3 25.1 1.0
CG C:PRO134 4.4 32.7 1.0
CG C:ARG133 4.4 51.9 1.0
O C:ALA132 4.4 29.5 1.0
C19 B:6XU202 4.4 32.5 1.0
C C:ARG133 4.6 29.9 1.0
O21 B:6XU202 4.6 32.2 1.0
C08 B:6XU202 4.7 27.7 1.0
C10 B:6XU202 4.7 23.4 1.0
C04 B:6XU202 4.7 22.7 1.0
CD1 C:TRP125 4.8 27.7 1.0
N C:ARG133 4.8 31.5 1.0
C06 B:6XU202 4.8 25.8 1.0
C C:ALA132 5.0 35.4 1.0

Fluorine binding site 9 out of 21 in 5gmz

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Fluorine binding site 9 out of 21 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:26.7
occ:1.00
 F34 B:6XU202 0.0 26.7 1.0
C31 B:6XU202 1.3 24.4 1.0
C32 B:6XU202 2.4 26.1 1.0
C30 B:6XU202 2.4 23.1 1.0
OG1 B:THR33 3.0 22.6 1.0
O B:ASP29 3.3 23.6 1.0
CB C:ARG127 3.3 23.9 1.0
C33 B:6XU202 3.6 24.2 1.0
C B:ASP29 3.6 22.3 1.0
C29 B:6XU202 3.7 24.4 1.0
CB B:PRO25 3.7 22.8 1.0
CD C:ARG127 3.8 23.1 1.0
CB B:ASP29 3.8 19.1 1.0
CG B:PRO25 3.9 22.0 1.0
CB B:THR33 4.0 26.2 1.0
N B:LEU30 4.0 20.7 1.0
O C:ARG127 4.1 28.4 1.0
CG C:ARG127 4.2 23.5 1.0
C28 B:6XU202 4.2 27.5 1.0
CA B:LEU30 4.3 21.2 1.0
CA B:ASP29 4.3 21.8 1.0
C C:ARG127 4.4 26.2 1.0
CA C:ARG127 4.5 24.1 1.0
CD2 B:LEU30 4.6 22.5 1.0
CG2 B:THR33 4.6 22.7 1.0
CG B:LEU30 4.8 22.2 1.0
O C:VAL124 4.9 25.5 1.0
CG B:ASP29 5.0 25.6 1.0

Fluorine binding site 10 out of 21 in 5gmz

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Fluorine binding site 10 out of 21 in the Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Hepatitis B Virus Core Protein Y132A Mutant in Complex with 4-Methyl Heteroaryldihydropyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:28.3
occ:1.00
 F22 C:6XU202 0.0 28.3 1.0
C16 C:6XU202 1.4 27.0 1.0
F23 C:6XU202 2.1 27.8 1.0
C15 C:6XU202 2.4 23.4 1.0
C17 C:6XU202 2.5 28.1 1.0
C18 C:6XU202 3.4 25.4 1.0
N14 C:6XU202 3.5 26.5 1.0
C13 C:6XU202 4.7 24.6 1.0
C19 C:6XU202 4.8 33.4 1.0

Reference:

Z.Qiu, X.Lin, M.Zhou, Y.Liu, W.Zhu, W.Chen, W.Zhang, L.Guo, H.Liu, G.Wu, M.Huang, M.Jiang, Z.Xu, Z.Zhou, N.Qin, S.Ren, H.Qiu, S.Zhong, Y.Zhang, Y.Zhang, X.Wu, L.Shi, F.Shen, Y.Mao, X.Zhou, W.Yang, J.Z.Wu, G.Yang, A.V.Mayweg, H.C.Shen, G.Tang. Design and Synthesis of Orally Bioavailable 4-Methyl Heteroaryldihydropyrimidine Based Hepatitis B Virus (Hbv) Capsid Inhibitors J.Med.Chem. V. 59 7651 2016.
ISSN: ISSN 0022-2623
PubMed: 27458651
DOI: 10.1021/ACS.JMEDCHEM.6B00879
Page generated: Thu Aug 1 09:40:19 2024

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