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Cadmium in PDB 6t8q: Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide

Enzymatic activity of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide

All present enzymatic activity of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide:
2.6.1.39; 2.6.1.7;

Protein crystallography data

The structure of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide, PDB code: 6t8q was solved by M.Blaesse, J.Venalainen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 125.43 / 2.51
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 144.829, 144.829, 139.653, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 21.6

Other elements in 6t8q:

The structure of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide (pdb code 6t8q). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide, PDB code: 6t8q:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 6t8q

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Cadmium binding site 1 out of 9 in the Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:0.5
occ:1.00
 NE2 A:HIS287 2.3 59.9 1.0
O A:HOH601 3.0 33.9 0.5
CD2 A:HIS287 3.2 46.6 1.0
O A:HOH666 3.3 46.2 1.0
CE1 A:HIS287 3.4 52.6 1.0
CG A:HIS287 4.4 46.4 1.0
ND1 A:HIS287 4.5 51.8 1.0
NZ A:LYS123 4.6 49.1 1.0
CB A:SER291 4.6 37.4 1.0
NH2 A:ARG14 4.8 47.3 1.0
OE2 A:GLU126 4.8 83.7 1.0
OG A:SER291 4.9 35.1 1.0
O A:HOH702 5.0 48.2 1.0

Cadmium binding site 2 out of 9 in 6t8q

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Cadmium binding site 2 out of 9 in the Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:51.7
occ:0.50
 OD1 A:ASP169 2.4 42.4 1.0
OE2 A:GLU215 2.4 62.9 1.0
OE1 A:GLU215 2.6 67.6 1.0
CD A:GLU215 2.9 62.6 1.0
CG A:ASP169 3.4 56.9 1.0
OD2 A:ASP169 3.6 59.5 1.0
NH1 A:ARG172 4.2 57.3 1.0
CG A:GLU215 4.4 65.8 1.0
NH2 A:ARG172 4.5 59.6 1.0
N A:ASP169 4.7 48.8 1.0
CB A:ASP169 4.8 50.2 1.0
OE2 A:GLU211 4.8 67.2 1.0
CZ A:ARG172 4.8 58.2 1.0
CG A:PRO168 4.9 47.4 1.0
OE1 A:GLU211 5.0 58.7 1.0

Cadmium binding site 3 out of 9 in 6t8q

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Cadmium binding site 3 out of 9 in the Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd504

b:0.8
occ:1.00
 OD1 A:ASP224 2.4 77.6 1.0
O A:HOH679 2.5 60.8 1.0
OD2 A:ASP224 2.8 82.6 1.0
CG A:ASP224 2.9 71.1 1.0
O A:GLU0 3.4 83.7 1.0
SD A:MET1 3.5 64.2 1.0
CA A:MET1 3.7 74.7 1.0
C A:GLU0 4.1 83.8 1.0
NH2 A:ARG254 4.2 52.4 1.0
N A:MET1 4.2 91.0 1.0
CG A:MET1 4.3 68.5 1.0
CB A:ASP224 4.3 64.2 1.0
N A:ASN2 4.4 69.3 1.0
CB A:MET1 4.4 72.8 1.0
C A:MET1 4.5 72.9 1.0
CE A:MET1 4.5 71.2 1.0
NH1 A:ARG254 4.8 52.4 1.0
CZ A:ARG254 5.0 50.3 1.0

Cadmium binding site 4 out of 9 in 6t8q

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Cadmium binding site 4 out of 9 in the Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd505

b:0.0
occ:1.00
 OD2 A:ASP324 2.4 96.2 1.0
OD2 A:ASP320 2.4 0.8 1.0
OD1 A:ASP324 3.0 71.3 1.0
CG A:ASP324 3.1 73.2 1.0
CG A:ASP320 3.4 78.7 1.0
OD1 A:ASP320 4.0 87.4 1.0
O A:ASP320 4.2 57.6 1.0
CB A:ASP320 4.5 71.5 1.0
CB A:ASP324 4.6 61.5 1.0
C A:ASP320 4.6 60.9 1.0

Cadmium binding site 5 out of 9 in 6t8q

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Cadmium binding site 5 out of 9 in the Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd506

b:0.1
occ:1.00
 NE2 A:HIS348 3.2 70.1 1.0
CD2 A:HIS348 3.5 67.0 1.0
O A:HOH737 3.7 54.9 1.0
O A:HOH744 3.8 57.2 1.0
O A:HOH641 4.0 52.6 1.0
O A:HOH750 4.4 56.4 1.0
N A:GLU163 4.4 49.4 1.0
CE1 A:HIS348 4.5 76.8 1.0
CA A:ASP162 4.6 45.4 1.0
C A:ASP162 4.7 43.7 1.0
CG A:HIS348 4.9 68.7 1.0

Cadmium binding site 6 out of 9 in 6t8q

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Cadmium binding site 6 out of 9 in the Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd507

b:0.0
occ:1.00
 O A:LEU149 2.5 54.4 1.0
SG A:CYS154 2.5 58.5 1.0
O A:CYS154 2.6 60.7 1.0
N A:CYS154 3.0 44.3 1.0
O A:HOH749 3.3 47.6 1.0
C A:CYS154 3.3 48.7 1.0
C A:LEU149 3.4 37.6 1.0
CA A:CYS154 3.5 52.6 1.0
CB A:CYS154 3.6 54.4 1.0
N A:GLY153 3.7 45.7 1.0
C A:GLY153 3.8 42.7 1.0
CA A:GLY153 4.0 42.7 1.0
CA A:HIS150 4.0 38.5 1.0
N A:HIS150 4.0 37.9 1.0
O A:HIS150 4.0 47.8 1.0
CB A:LEU149 4.2 37.4 1.0
C A:HIS150 4.3 43.2 1.0
CA A:LEU149 4.3 41.0 1.0
CD1 A:ILE156 4.4 50.4 1.0
CG1 A:ILE156 4.5 47.7 1.0
N A:ASN155 4.5 52.2 1.0
C A:LEU152 4.5 43.6 1.0
O A:GLY153 4.7 47.1 1.0
O A:HOH719 4.8 46.6 1.0
N A:LEU152 4.9 44.7 1.0
CB A:LEU152 5.0 39.0 1.0

Cadmium binding site 7 out of 9 in 6t8q

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Cadmium binding site 7 out of 9 in the Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd508

b:0.7
occ:1.00
 OD1 A:ASP110 2.5 91.2 1.0
O A:HOH724 3.0 60.9 1.0
O A:HOH748 3.1 59.4 1.0
O A:HOH757 3.2 49.5 1.0
CG A:ASP110 3.6 57.3 1.0
O A:LEU111 4.1 44.7 1.0
O A:HOH668 4.2 54.9 1.0
N A:LEU111 4.2 47.2 1.0
OD2 A:ASP110 4.3 66.8 1.0
CA A:ASP110 4.6 52.3 1.0
CB A:ASP110 4.7 60.4 1.0
O A:HOH746 4.9 50.8 1.0
C A:ASP110 4.9 46.6 1.0
C A:LEU111 5.0 45.2 1.0

Cadmium binding site 8 out of 9 in 6t8q

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Cadmium binding site 8 out of 9 in the Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd509

b:84.2
occ:0.50
 CD A:CD509 0.0 84.2 0.5
OE2 A:GLU282 2.4 74.5 0.5
OE1 A:GLU282 2.5 88.3 0.5
CD A:GLU282 2.8 73.2 0.5
OE2 A:GLU282 3.0 0.8 0.5
CD A:CD509 3.4 0.6 0.5
CD A:GLU282 3.7 91.3 0.5
O A:HOH683 3.7 52.4 1.0
OE1 A:GLU282 4.0 92.6 0.5
CG A:GLU282 4.3 68.7 0.5
NH2 A:ARG283 4.5 45.5 1.0
CG A:GLU282 4.8 79.2 0.5

Cadmium binding site 9 out of 9 in 6t8q

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Cadmium binding site 9 out of 9 in the Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Hkatii in Complex with Ligand (2R)-N-Benzyl-1-[6-Methyl-5-(Oxan-4-Yl)- 7-Oxo-6H,7H-[1,3]Thiazolo[5,4-D]Pyrimidin-2-Yl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd509

b:0.6
occ:0.50
 CD A:CD509 0.0 0.6 0.5
OE1 A:GLU282 2.4 92.6 0.5
OE1 A:GLU282 2.6 88.3 0.5
CD A:GLU282 3.3 91.3 0.5
CD A:CD509 3.4 84.2 0.5
OE2 A:GLU282 3.5 0.8 0.5
CD A:GLU282 3.7 73.2 0.5
CE A:LYS278 4.1 79.6 1.0
CG A:LYS278 4.2 61.1 1.0
OE2 A:GLU282 4.4 74.5 0.5
CG A:GLU282 4.5 68.7 0.5
CD A:LYS278 4.6 76.4 1.0
CG A:GLU282 4.7 79.2 0.5
CB A:PRO104 4.8 69.8 1.0
CB A:GLU282 4.9 58.8 0.5
CB A:GLU282 4.9 64.1 0.5
NZ A:LYS278 5.0 76.2 1.0

Reference:

T.Kalliokoski, P.Rummakko, M.Rantanen, M.Blaesse, M.Augustin, G.R.Ummenthala, S.Choudhary, J.Venalainen. Discovery of Sulfonamides and 9-Oxo-2,8-Diazaspiro[5,5]Undecane-2-Carboxamides As Human Kynurenine Aminotransferase 2 (KAT2) Inhibitors Bioorg.Med.Chem.Lett. 2020.
ISSN: ESSN 1464-3405
DOI: 10.1016/J.BMCL.2020.127060
Page generated: Fri Jul 19 19:41:48 2024

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