Atomistry » Fluorine » PDB 5g48-5he1 » 5gmz
Atomistry »
  Fluorine »
    PDB 5g48-5he1 »
      5gmz »

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

Go back to Fluorine Binding Sites List in 5gmz
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

Go back to Fluorine Binding Sites List in 5gmz
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

Go back to Fluorine Binding Sites List in 5gmz
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

Go back to Fluorine Binding Sites List in 5gmz
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

Go back to Fluorine Binding Sites List in 5gmz
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

Go back to Fluorine Binding Sites List in 5gmz
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

Go back to Fluorine Binding Sites List in 5gmz
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

Go back to Fluorine Binding Sites List in 5gmz
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

Go back to Fluorine Binding Sites List in 5gmz
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

Go back to Fluorine Binding Sites List in 5gmz
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy