Chlorine in PDB 7k5m: Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution

Protein crystallography data

The structure of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution, PDB code: 7k5m was solved by S.D.Kuduk, B.Stoops, R.Alexander, A.M.Lam, C.Espiritu, R.Vogel, V.Lau, K.Klumpp, O.A.Flores, G.D.Hartman, C.M.Lukacs, J.Abendroth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.04 / 2.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 151.58, 87.96, 106.71, 90, 103.53, 90
R / Rfree (%) 24.2 / 27.6

Other elements in 7k5m:

The structure of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution (pdb code 7k5m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution, PDB code: 7k5m:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7k5m

Go back to Chlorine Binding Sites List in 7k5m
Chlorine binding site 1 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:62.0
occ:0.80
 CL07 A:VXJ201 0.0 62.0 0.8
C06 A:VXJ201 1.8 69.4 1.0
C05 A:VXJ201 2.7 73.1 1.0
C08 A:VXJ201 2.8 64.3 1.0
OG1 A:THR33 3.0 49.1 1.0
F09 A:VXJ201 3.0 74.8 1.0
O A:ASP29 3.7 48.5 1.0
CB A:THR33 3.8 48.2 1.0
CD2 A:LEU30 3.8 53.9 1.0
CG A:PRO25 3.9 52.3 1.0
CG2 A:THR33 4.0 49.2 1.0
C04 A:VXJ201 4.0 60.6 1.0
C10 A:VXJ201 4.1 55.8 1.0
CB A:PRO25 4.1 56.0 1.0
C A:ASP29 4.2 63.1 1.0
CA A:LEU30 4.4 63.8 1.0
N A:LEU30 4.5 63.2 1.0
C11 A:VXJ201 4.6 55.8 1.0
CG A:LEU30 4.7 60.4 1.0
CB A:ASP29 4.7 61.3 1.0

Chlorine binding site 2 out of 6 in 7k5m

Go back to Chlorine Binding Sites List in 7k5m
Chlorine binding site 2 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:55.8
occ:0.70
 CL07 B:VXJ201 0.0 55.8 0.7
C06 B:VXJ201 1.8 58.7 1.0
C05 B:VXJ201 2.7 62.1 1.0
C08 B:VXJ201 2.8 57.9 1.0
F09 B:VXJ201 3.0 57.0 1.0
OG1 B:THR33 3.2 64.9 1.0
CD2 B:LEU30 3.7 61.8 1.0
CG B:PRO25 3.8 63.1 1.0
O B:ASP29 3.9 70.7 1.0
CB B:THR33 3.9 64.7 1.0
C04 B:VXJ201 4.0 56.1 1.0
C10 B:VXJ201 4.1 55.8 1.0
CB C:ARG127 4.1 71.8 1.0
CB B:PRO25 4.1 63.1 1.0
CG2 B:THR33 4.1 65.2 1.0
C B:ASP29 4.4 73.3 1.0
CD C:ARG127 4.4 72.6 1.0
CA B:LEU30 4.4 68.3 1.0
C11 B:VXJ201 4.6 55.8 1.0
CG B:LEU30 4.6 64.5 1.0
N B:LEU30 4.6 70.6 1.0
CG C:ARG127 4.8 67.7 1.0
O C:VAL124 4.9 67.8 1.0
CB B:ASP29 4.9 74.6 1.0

Chlorine binding site 3 out of 6 in 7k5m

Go back to Chlorine Binding Sites List in 7k5m
Chlorine binding site 3 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl500

b:78.0
occ:0.81
 CL07 C:VXJ500 0.0 78.0 0.8
C06 C:VXJ500 1.8 78.2 1.0
C05 C:VXJ500 2.7 72.4 1.0
C08 C:VXJ500 2.8 66.5 1.0
F09 C:VXJ500 3.0 64.4 1.0
OG1 C:THR33 3.2 66.3 1.0
CD2 C:LEU30 3.5 76.2 1.0
CG C:PRO25 3.7 68.7 1.0
O C:ASP29 3.8 84.4 1.0
CB C:THR33 3.9 65.6 1.0
CB C:PRO25 3.9 68.5 1.0
CG2 C:THR33 4.0 66.6 1.0
C04 C:VXJ500 4.0 60.3 1.0
C10 C:VXJ500 4.1 57.0 1.0
CA C:LEU30 4.3 71.5 1.0
C C:ASP29 4.3 84.4 1.0
CG C:LEU30 4.4 77.4 1.0
N C:LEU30 4.5 77.5 1.0
C11 C:VXJ500 4.6 55.8 1.0
CD C:PRO25 4.9 73.2 1.0
CB C:ASP29 4.9 78.8 1.0
CB C:LEU30 4.9 81.4 1.0

Chlorine binding site 4 out of 6 in 7k5m

Go back to Chlorine Binding Sites List in 7k5m
Chlorine binding site 4 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl201

b:58.4
occ:0.74
 CL07 D:VXJ201 0.0 58.4 0.7
C06 D:VXJ201 1.8 63.2 1.0
C05 D:VXJ201 2.7 61.5 1.0
C08 D:VXJ201 2.8 57.8 1.0
OG1 D:THR33 3.0 65.9 1.0
F09 D:VXJ201 3.0 67.1 1.0
O D:ASP29 3.7 65.8 1.0
CB D:THR33 3.7 65.7 1.0
CG2 D:THR33 4.0 65.8 1.0
CG D:PRO25 4.0 64.9 1.0
CD2 D:LEU30 4.0 69.8 1.0
C04 D:VXJ201 4.0 58.6 1.0
CB E:ARG127 4.0 73.3 1.0
C10 D:VXJ201 4.1 55.8 1.0
CB D:PRO25 4.3 64.7 1.0
C D:ASP29 4.3 74.7 1.0
CD E:ARG127 4.4 68.4 1.0
CA D:LEU30 4.5 64.6 1.0
C11 D:VXJ201 4.6 55.8 1.0
N D:LEU30 4.7 77.4 1.0
O E:VAL124 4.7 70.6 1.0
CG E:ARG127 4.8 66.3 1.0
CG D:LEU30 4.9 69.8 1.0
CB D:ASP29 5.0 81.6 1.0
CA E:VAL124 5.0 82.8 1.0

Chlorine binding site 5 out of 6 in 7k5m

Go back to Chlorine Binding Sites List in 7k5m
Chlorine binding site 5 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl201

b:65.1
occ:0.78
 CL07 E:VXJ201 0.0 65.1 0.8
C06 E:VXJ201 1.8 72.0 1.0
C05 E:VXJ201 2.7 71.2 1.0
C08 E:VXJ201 2.8 64.3 1.0
F09 E:VXJ201 3.0 71.5 1.0
OG1 E:THR33 3.2 60.9 1.0
CD2 E:LEU30 3.7 64.0 1.0
O E:ASP29 3.8 67.3 1.0
CG E:PRO25 3.8 62.9 1.0
CB E:THR33 3.9 60.6 1.0
CB E:PRO25 4.0 62.6 1.0
C04 E:VXJ201 4.0 58.5 1.0
C10 E:VXJ201 4.1 55.8 1.0
CG2 E:THR33 4.1 61.1 1.0
C E:ASP29 4.3 73.8 1.0
CA E:LEU30 4.4 71.2 1.0
N E:LEU30 4.6 78.8 1.0
C11 E:VXJ201 4.6 55.8 1.0
CG E:LEU30 4.6 60.7 1.0
CB E:ASP29 4.9 72.9 1.0

Chlorine binding site 6 out of 6 in 7k5m

Go back to Chlorine Binding Sites List in 7k5m
Chlorine binding site 6 out of 6 in the Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Hbv Capsid Y132A Mutant in Complex with N-(3- Chloro-4-Fluorophenyl)-3-Phenyl-1,4,6,7-Tetrahydro-5H-Pyrazolo[4,3- C]Pyridine-5-Carboxamide at 2.65A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl500

b:63.0
occ:0.72
 CL07 F:VXJ500 0.0 63.0 0.7
C06 F:VXJ500 1.8 70.0 1.0
C05 F:VXJ500 2.8 69.2 1.0
C08 F:VXJ500 2.8 57.8 1.0
F09 F:VXJ500 3.0 55.8 1.0
OG1 F:THR33 3.4 60.3 1.0
CD2 F:LEU30 3.6 57.3 1.0
CG F:PRO25 3.7 57.6 1.0
CB F:PRO25 4.0 61.8 1.0
O F:ASP29 4.0 59.9 1.0
C04 F:VXJ500 4.0 57.5 1.0
C10 F:VXJ500 4.1 55.8 1.0
CB A:ARG127 4.1 62.1 1.0
CB F:THR33 4.2 59.6 1.0
CG2 F:THR33 4.4 60.2 1.0
CA F:LEU30 4.5 65.6 1.0
C F:ASP29 4.5 66.3 1.0
C11 F:VXJ500 4.6 55.8 1.0
CG F:LEU30 4.6 64.0 1.0
CD A:ARG127 4.6 49.5 1.0
N F:LEU30 4.7 58.0 1.0
O A:VAL124 4.9 50.0 1.0
CG A:ARG127 5.0 49.1 1.0
O A:ARG127 5.0 71.5 1.0
C A:ARG127 5.0 62.8 1.0
CD F:PRO25 5.0 78.0 1.0

Reference:

S.D.Kuduk, B.Stoops, R.Alexander, A.M.Lam, C.Espiritu, R.Vogel, V.Lau, K.Klumpp, O.A.Flores, G.D.Hartman. Identification of A New Class of Hbv Capsid Assembly Modulator. Bioorg.Med.Chem.Lett. V. 39 27848 2021.
ISSN: ESSN 1464-3405
PubMed: 33610748
DOI: 10.1016/J.BMCL.2021.127848
Page generated: Mon Jul 29 23:22:33 2024

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