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Iodine in PDB 6t8p: 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: 6t8p 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) 74.45 / 2.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.057, 96.936, 116.260, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.2

Other elements in 6t8p:

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:

Fluorine (F) 12 atoms

Iodine Binding Sites:

The binding sites of Iodine 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 6t8p). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine 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: 6t8p:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 6t8p

Go back to Iodine Binding Sites List in 6t8p
Iodine binding site 1 out of 7 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 Iodine with other atoms in the I 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:I504

b:23.7
occ:1.00
 NZ B:LYS123 3.4 31.0 1.0
NZ A:LYS123 3.5 30.9 1.0
NE2 B:GLN119 3.6 22.7 1.0
CE A:LYS123 3.7 26.4 1.0
NE2 A:GLN119 3.8 22.1 1.0
OG B:SER291 3.8 25.1 1.0
O A:HOH650 3.9 27.1 1.0
OG A:SER291 3.9 24.6 1.0
CE B:LYS123 3.9 30.7 1.0
CB B:SER291 3.9 22.2 1.0
CB A:SER291 4.0 22.4 1.0
O B:HOH644 4.0 28.1 1.0
CG2 A:THR292 4.2 18.5 1.0
CG B:GLN119 4.2 20.1 1.0
CG A:GLN119 4.3 21.3 1.0
CG2 B:THR292 4.3 20.3 1.0
CD B:GLN119 4.4 20.6 1.0
CD A:GLN119 4.5 21.3 1.0
CD B:LYS123 4.8 32.5 1.0
N B:THR292 4.8 20.4 1.0
N A:THR292 4.9 19.3 1.0

Iodine binding site 2 out of 7 in 6t8p

Go back to Iodine Binding Sites List in 6t8p
Iodine binding site 2 out of 7 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 Iodine with other atoms in the I 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:I505

b:71.3
occ:1.00
 OG A:SER304 3.3 24.4 1.0
CB A:SER304 3.8 24.4 1.0
N A:GLN305 4.0 25.3 1.0
CB A:GLU82 4.0 26.7 1.0
NE2 A:GLN305 4.0 56.6 1.0
C A:SER304 4.0 24.8 1.0
CG A:GLN305 4.1 38.5 1.0
CG A:GLU82 4.1 29.1 1.0
ND1 A:HIS308 4.2 27.1 1.0
O A:SER304 4.3 23.8 1.0
CA A:GLN305 4.3 26.3 1.0
CA A:SER304 4.5 23.7 1.0
CE1 A:HIS308 4.6 28.4 1.0
CD2 A:LEU301 4.6 23.9 1.0
CD A:GLN305 4.6 45.2 1.0
CD A:GLU82 4.7 30.2 1.0
CB A:GLN305 4.8 32.3 1.0
CG A:HIS308 4.9 27.4 1.0
O A:LEU301 4.9 22.5 1.0

Iodine binding site 3 out of 7 in 6t8p

Go back to Iodine Binding Sites List in 6t8p
Iodine binding site 3 out of 7 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 Iodine with other atoms in the I 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:I506

b:54.2
occ:0.50
 O A:HOH754 3.4 35.6 1.0
NE1 A:TRP86 3.5 23.4 1.0
CA A:GLY311 4.0 24.9 1.0
CD1 A:TRP86 4.0 23.3 1.0
CD2 A:HIS308 4.0 28.3 1.0
CA A:HIS308 4.1 27.6 1.0
O A:HIS308 4.1 28.4 1.0
O A:LEU307 4.3 24.3 1.0
CG A:HIS308 4.5 27.4 1.0
C A:HIS308 4.6 28.8 1.0
N A:GLY311 4.6 23.9 1.0
CB A:HIS308 4.7 28.1 1.0
CE2 A:TRP86 4.7 21.6 1.0
NE2 A:HIS308 4.8 28.3 1.0
C A:GLY311 4.9 24.6 1.0
N A:GLU312 4.9 24.0 1.0
N A:HIS308 4.9 24.7 1.0
C A:LEU307 5.0 25.0 1.0

Iodine binding site 4 out of 7 in 6t8p

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Iodine binding site 4 out of 7 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 Iodine with other atoms in the I 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:I507

b:89.5
occ:0.50
 OG A:SER77 3.7 22.5 0.5
N A:SER77 3.8 23.7 0.5
N A:SER77 3.8 22.7 0.5
O A:HOH796 3.9 25.8 1.0
CA A:PRO76 4.0 23.8 1.0
CB A:PRO76 4.2 24.6 1.0
CB A:SER77 4.4 26.4 0.5
C A:PRO76 4.4 23.7 1.0
O A:HOH739 4.5 36.5 1.0
CB A:SER77 4.5 23.2 0.5
C28 A:MVT502 4.6 44.7 1.0
NE2 A:GLN289 4.6 32.6 1.0
C22 A:MVT502 4.8 50.9 1.0
CA A:SER77 4.8 24.2 0.5
CA A:SER77 4.8 22.5 0.5
C30 A:MVT502 4.8 41.5 1.0

Iodine binding site 5 out of 7 in 6t8p

Go back to Iodine Binding Sites List in 6t8p
Iodine binding site 5 out of 7 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 Iodine with other atoms in the I 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
B:I502

b:30.1
occ:1.00
 O B:HOH712 3.4 25.6 1.0
CD B:PRO81 3.7 22.6 1.0
N B:MET33 3.7 40.2 1.0
NH2 B:ARG70 3.7 24.1 1.0
CG B:MET33 3.9 43.7 1.0
CD B:PRO76 3.9 19.9 1.0
C13 B:MVT501 4.0 33.4 1.0
CG B:PRO81 4.0 24.4 1.0
F17 B:MVT501 4.1 27.4 1.0
CB B:MET33 4.1 42.9 1.0
CG B:PRO76 4.2 20.5 1.0
CA B:SER32 4.3 39.5 1.0
OG B:SER32 4.5 41.2 1.0
C12 B:MVT501 4.5 30.1 1.0
NE B:ARG70 4.5 22.8 1.0
C B:SER32 4.5 39.9 1.0
CZ B:ARG70 4.5 23.3 1.0
CA B:MET33 4.5 41.9 1.0
CG2 B:ILE80 4.9 18.9 1.0
CB B:SER32 4.9 39.9 1.0
O B:LYS31 4.9 38.4 1.0
C14 B:MVT501 5.0 32.6 1.0

Iodine binding site 6 out of 7 in 6t8p

Go back to Iodine Binding Sites List in 6t8p
Iodine binding site 6 out of 7 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 Iodine with other atoms in the I 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
B:I503

b:0.5
occ:1.00
 CG B:LYS278 4.1 26.3 1.0
CA B:PRO279 4.1 22.3 1.0
N B:PRO279 4.1 22.2 1.0
CG B:PRO279 4.1 24.9 1.0
CB B:PRO104 4.2 31.7 1.0
O B:PRO104 4.3 32.4 1.0
C B:PRO104 4.4 31.8 1.0
CD B:LYS278 4.4 30.0 1.0
C B:LYS278 4.5 23.0 1.0
CB B:PRO279 4.5 23.4 1.0
CG B:GLU282 4.5 45.9 1.0
CD B:PRO279 4.6 23.2 1.0
CB B:LYS278 4.6 25.0 1.0
O B:LYS278 4.7 20.9 1.0
N B:SER105 4.8 34.1 1.0
CE B:LYS278 4.8 32.0 1.0
CA B:PRO104 4.8 32.8 1.0
O B:HOH779 4.9 48.4 1.0

Iodine binding site 7 out of 7 in 6t8p

Go back to Iodine Binding Sites List in 6t8p
Iodine binding site 7 out of 7 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 Iodine with other atoms in the I 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
B:I504

b:94.2
occ:1.00
 NE B:ARG321 3.4 31.9 1.0
CG B:GLU56 3.8 25.8 1.0
NH2 B:ARG321 3.8 30.2 1.0
CD B:GLU56 3.8 26.0 1.0
O2 B:EDO506 3.8 39.9 1.0
CZ B:ARG321 3.8 31.7 1.0
CB B:GLU56 3.9 24.8 1.0
OE2 B:GLU56 4.0 25.0 1.0
CB B:ASN57 4.2 31.6 1.0
CD B:ARG321 4.2 32.2 1.0
OE1 B:GLU56 4.3 27.1 1.0
N B:ASN57 4.3 28.4 1.0
O B:HOH723 4.4 42.0 1.0
O B:HOH839 4.5 45.2 1.0
C B:GLU56 4.7 26.5 1.0
CA B:ASN57 4.7 30.5 1.0
NH1 B:ARG321 4.8 32.9 1.0
C2 B:EDO506 4.8 44.3 1.0
CG B:ASN57 4.8 34.9 1.0
CA B:GLU56 4.9 24.8 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: Mon Aug 12 00:19:44 2024

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