Chlorine in PDB 8tcu: Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid

Enzymatic activity of Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid

All present enzymatic activity of Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid:
1.5.1.2;

Protein crystallography data

The structure of Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid, PDB code: 8tcu was solved by J.J.Tanner, K.R.Meeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 89.46 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.009, 178.914, 88.078, 90, 107.12, 90
R / Rfree (%) 18.9 / 21.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid (pdb code 8tcu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid, PDB code: 8tcu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8tcu

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Chlorine binding site 1 out of 5 in the Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:29.2
occ:1.00
 CL06 A:ZR3401 0.0 29.2 1.0
C05 A:ZR3401 1.8 26.9 1.0
C07 A:ZR3401 2.7 25.6 1.0
C04 A:ZR3401 2.8 26.2 1.0
O01 A:ZR3401 3.1 24.2 1.0
C02 A:ZR3401 3.1 27.8 1.0
OG1 A:THR238 3.1 24.7 1.0
OG B:SER176 3.3 24.2 1.0
CG2 B:THR171 3.6 23.7 1.0
C B:GLY175 3.8 22.1 1.0
N B:SER176 3.9 23.1 1.0
O B:GLY175 4.0 22.3 1.0
C08 A:ZR3401 4.0 29.5 1.0
C10 A:ZR3401 4.0 27.5 1.0
O03 A:ZR3401 4.1 27.1 1.0
O B:THR171 4.1 20.0 1.0
CB A:ALA237 4.2 22.2 1.0
CA B:GLY175 4.2 21.4 1.0
CA B:SER176 4.3 23.5 1.0
CB B:SER176 4.4 23.7 1.0
N A:THR238 4.4 19.5 1.0
CB A:THR238 4.4 24.2 1.0
C09 A:ZR3401 4.5 29.1 1.0
OG B:SER261 4.8 20.1 1.0
C B:THR171 4.8 18.8 1.0
CA A:THR238 4.9 22.2 1.0
SD B:MET121 4.9 27.7 1.0
CB B:THR171 4.9 24.4 1.0

Chlorine binding site 2 out of 5 in 8tcu

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Chlorine binding site 2 out of 5 in the Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:28.1
occ:1.00
 CL06 B:ZR3401 0.0 28.1 1.0
C05 B:ZR3401 1.8 27.8 1.0
C07 B:ZR3401 2.7 24.7 1.0
C04 B:ZR3401 2.8 27.5 1.0
OG1 B:THR238 3.1 23.7 1.0
O03 B:ZR3401 3.1 24.6 1.0
C02 B:ZR3401 3.1 26.4 1.0
OG A:SER176 3.4 23.9 1.0
CG2 A:THR171 3.6 23.2 1.0
C A:GLY175 3.7 23.8 1.0
N A:SER176 3.8 22.8 1.0
O A:GLY175 3.9 22.4 1.0
C08 B:ZR3401 4.0 24.2 1.0
C10 B:ZR3401 4.0 27.1 1.0
O A:THR171 4.1 21.9 1.0
O01 B:ZR3401 4.1 24.1 1.0
CA A:GLY175 4.2 21.6 1.0
CA A:SER176 4.2 20.7 1.0
CB B:ALA237 4.3 23.1 1.0
CB B:THR238 4.4 23.0 1.0
CB A:SER176 4.4 22.3 1.0
N B:THR238 4.4 24.4 1.0
C09 B:ZR3401 4.5 26.9 1.0
OG A:SER261 4.7 21.3 1.0
CA B:THR238 4.8 22.3 1.0
C A:THR171 4.9 22.2 1.0
SD A:MET121 4.9 24.7 1.0
CB A:THR171 5.0 22.8 1.0

Chlorine binding site 3 out of 5 in 8tcu

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Chlorine binding site 3 out of 5 in the Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:33.1
occ:1.00
 CL06 C:ZR3401 0.0 33.1 1.0
C05 C:ZR3401 1.8 29.1 1.0
C07 C:ZR3401 2.7 29.4 1.0
C04 C:ZR3401 2.8 29.0 1.0
OG1 C:THR238 3.1 25.5 1.0
O01 C:ZR3401 3.1 28.3 1.0
C02 C:ZR3401 3.2 28.5 1.0
OG D:SER176 3.2 21.2 1.0
CG2 D:THR171 3.4 25.7 1.0
N D:SER176 3.7 24.3 1.0
C D:GLY175 3.8 27.4 1.0
C08 C:ZR3401 4.0 33.0 1.0
C10 C:ZR3401 4.0 32.4 1.0
O D:GLY175 4.1 26.1 1.0
O D:THR171 4.1 23.0 1.0
CA D:SER176 4.1 25.8 1.0
O03 C:ZR3401 4.1 25.9 1.0
CB C:ALA237 4.2 25.4 1.0
CA D:GLY175 4.2 23.1 1.0
CB D:SER176 4.3 26.7 1.0
N C:THR238 4.3 26.0 1.0
CB C:THR238 4.4 27.0 1.0
C09 C:ZR3401 4.5 34.0 1.0
OG D:SER261 4.7 23.9 1.0
C D:THR171 4.8 24.8 1.0
CB D:THR171 4.8 23.1 1.0
CA C:THR238 4.8 22.4 1.0
C C:ALA237 5.0 23.7 1.0

Chlorine binding site 4 out of 5 in 8tcu

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Chlorine binding site 4 out of 5 in the Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:35.6
occ:1.00
 CL06 D:ZR3401 0.0 35.6 1.0
C05 D:ZR3401 1.8 34.0 1.0
C07 D:ZR3401 2.7 34.3 1.0
C04 D:ZR3401 2.8 35.5 1.0
C02 D:ZR3401 3.1 32.9 1.0
OG1 D:THR238 3.2 27.0 1.0
O03 D:ZR3401 3.2 30.6 1.0
OG C:SER176 3.3 24.2 1.0
CG2 C:THR171 3.6 28.6 1.0
C C:GLY175 3.9 23.8 1.0
N C:SER176 4.0 25.3 1.0
C08 D:ZR3401 4.0 37.2 1.0
C10 D:ZR3401 4.0 34.7 1.0
O C:GLY175 4.0 25.3 1.0
O01 D:ZR3401 4.1 30.1 1.0
CB D:ALA237 4.1 23.5 1.0
O C:THR171 4.1 24.1 1.0
CA C:GLY175 4.3 23.4 1.0
CA C:SER176 4.3 25.5 1.0
N D:THR238 4.4 21.7 1.0
CB C:SER176 4.4 23.0 1.0
CB D:THR238 4.5 25.0 1.0
C09 D:ZR3401 4.5 37.2 1.0
OG C:SER261 4.7 24.2 1.0
CA D:THR238 4.9 22.9 1.0
C C:THR171 4.9 24.5 1.0
CB C:THR171 4.9 26.8 1.0
SD C:MET121 5.0 30.3 1.0

Chlorine binding site 5 out of 5 in 8tcu

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Chlorine binding site 5 out of 5 in the Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of PYCR1 Complexed with 2-Chloro-5-(2-Oxoimidazolidin-1-Yl) Benzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:31.7
occ:1.00
 CL06 E:ZR3401 0.0 31.7 1.0
C05 E:ZR3401 1.8 29.8 1.0
C07 E:ZR3401 2.7 31.4 1.0
C04 E:ZR3401 2.8 28.9 1.0
C02 E:ZR3401 3.1 27.5 1.0
OG1 E:THR238 3.1 25.8 1.0
O01 E:ZR3401 3.2 27.4 1.0
C08 E:ZR3401 4.0 31.0 1.0
O03 E:ZR3401 4.0 26.2 1.0
C10 E:ZR3401 4.1 27.6 1.0
CB E:ALA237 4.2 22.2 1.0
CB E:THR238 4.4 23.6 1.0
N E:THR238 4.4 21.4 1.0
C09 E:ZR3401 4.5 31.7 1.0
CA E:THR238 4.9 23.4 1.0

Reference:

K.R.Meeks, J.Ji, M.V.Protopopov, O.O.Tarkhanova, Y.S.Moroz, J.J.Tanner. Novel Fragment Inhibitors of PYCR1 From Docking-Guided X-Ray Crystallography. J.Chem.Inf.Model. 2024.
ISSN: ESSN 1549-960X
PubMed: 38411104
DOI: 10.1021/ACS.JCIM.3C01879
Page generated: Tue Jul 30 12:47:29 2024

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