Iodine in PDB 6ft7: Crystal Structure of CLK3 in Complex with Compound 8A

All present enzymatic activity of Crystal Structure of CLK3 in Complex with Compound 8A:
2.7.12.1;

The structure of Crystal Structure of CLK3 in Complex with Compound 8A, PDB code: 6ft7 was solved by A.Chaikuad, A.Walter, F.Von Delft, C.Bountra, C.H.Arrowsmith, A.M.Edwards, C.Kunick, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.41 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.760, 116.830, 69.910, 90.00, 92.75, 90.00
R / Rfree (%)	19.2 / 23.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of CLK3 in Complex with Compound 8A (pdb code 6ft7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 14 binding sites of Iodine where determined in the Crystal Structure of CLK3 in Complex with Compound 8A, PDB code: 6ft7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 14 in the Crystal Structure of CLK3 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of CLK3 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:68.3 occ:0.90 OD1 A:ASP447 3.8 47.7 1.0 CB A:ASP447 3.9 43.8 1.0 CE1 A:HIS469 4.0 37.0 1.0 CG A:ASP447 4.0 46.8 1.0 CG A:GLN444 4.0 45.1 1.0 NE2 A:HIS469 4.2 37.2 1.0 CA A:GLN444 4.2 42.3 1.0 CB A:GLN444 4.4 44.0 1.0 CG A:PRO470 4.4 44.0 1.0 CB A:PRO470 4.5 44.2 1.0 OD2 A:ASP447 4.8 49.2 1.0 NE2 A:GLN444 4.8 46.4 1.0 CD A:PRO470 4.8 41.6 1.0 CD A:GLN444 4.9 45.5 1.0 NH1 A:ARG451 5.0 75.9 1.0

Iodine binding site 2 out of 14 in the Crystal Structure of CLK3 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of CLK3 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:58.2 occ:0.75 ND2 A:ASN203 3.5 33.3 1.0 N B:ASN227 3.6 36.7 1.0 NZ A:LYS206 3.7 44.1 1.0 CD A:LYS207 4.0 40.6 1.0 CB B:PHE226 4.0 36.9 1.0 CA B:PHE226 4.0 36.1 1.0 CB A:LYS207 4.1 33.8 1.0 CB B:ASN227 4.3 40.6 1.0 C B:PHE226 4.4 35.8 1.0 CA B:ASN227 4.5 39.1 1.0 CA A:LYS207 4.5 31.6 1.0 O B:ASN227 4.5 38.0 1.0 O A:ASN203 4.7 25.8 1.0 CG A:LYS207 4.7 36.7 1.0 CG A:ASN203 4.7 32.0 1.0 N A:LYS207 4.7 30.6 1.0 OE1 A:GLU210 4.8 53.2 1.0 O A:HOH667 4.8 44.6 1.0 CE A:LYS206 4.9 44.4 1.0 CD A:LYS206 4.9 42.5 1.0 C B:ASN227 4.9 39.7 1.0

Iodine binding site 3 out of 14 in the Crystal Structure of CLK3 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of CLK3 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:64.6 occ:0.80 NE2 A:GLN375 3.4 27.6 1.0 O A:THR376 4.0 34.3 1.0 C A:THR376 4.0 36.0 1.0 CG A:GLN375 4.1 28.5 1.0 O A:GLN375 4.1 34.8 1.0 CE1 A:HIS339 4.1 40.2 1.0 N A:THR376 4.1 34.5 1.0 C A:GLN375 4.2 32.5 1.0 CD A:GLN375 4.2 29.2 1.0 CB A:HIS377 4.4 42.6 1.0 CA A:THR376 4.4 35.0 1.0 N A:HIS377 4.5 35.4 1.0 NE2 A:HIS339 4.6 41.5 1.0 CA A:GLN375 4.9 30.9 1.0 CA A:HIS377 4.9 38.2 1.0

Iodine binding site 4 out of 14 in the Crystal Structure of CLK3 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of CLK3 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:55.9 occ:0.70 N A:LEU144 3.3 48.0 1.0 O A:ILE187 3.5 37.6 1.0 CA A:HIS143 3.5 55.6 1.0 CB A:HIS143 3.8 56.4 1.0 CA A:GLY168 3.8 40.2 1.0 N A:ARG189 3.9 44.7 1.0 CD2 A:HIS143 3.9 57.7 1.0 C A:HIS143 3.9 52.5 1.0 CG2 A:ILE187 3.9 35.3 1.0 C A:ILE188 4.0 41.0 1.0 CA A:ARG189 4.0 45.5 1.0 O A:ILE188 4.0 41.2 1.0 CG A:HIS143 4.0 59.1 1.0 CE A:LYS169 4.1 57.8 1.0 CG A:ARG189 4.1 51.3 1.0 C A:ILE187 4.2 35.9 1.0 N A:LYS169 4.2 38.7 1.0 ND1 A:HIS231 4.3 36.2 1.0 CB A:LEU144 4.3 44.7 1.0 C A:GLY168 4.4 39.5 1.0 CA A:LEU144 4.4 48.1 1.0 CB A:ILE187 4.5 35.4 1.0 CG A:LYS169 4.5 49.7 1.0 O A:GLY142 4.6 51.4 1.0 CE1 A:HIS231 4.6 38.0 1.0 CB A:ARG189 4.7 49.0 1.0 O A:LEU144 4.7 53.6 1.0 N A:HIS143 4.7 55.7 1.0 N A:ILE188 4.8 37.1 1.0 CA A:ILE188 4.8 38.2 1.0 CD A:LYS169 4.9 54.2 1.0 CB A:LYS169 5.0 44.2 1.0 CA A:ILE187 5.0 33.6 1.0 NE2 A:HIS143 5.0 58.8 1.0

Iodine binding site 5 out of 14 in the Crystal Structure of CLK3 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of CLK3 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:0.5 occ:0.90 CD A:LYS405 3.5 72.2 1.0 CG A:LYS405 3.8 68.7 1.0 CE A:LYS405 3.8 76.2 1.0 O A:ARG402 3.9 53.2 1.0 CA A:LYS403 4.0 54.4 1.0 CB A:LYS405 4.1 66.5 1.0 N A:GLN404 4.1 57.3 1.0 N A:LYS405 4.2 57.0 1.0 NZ A:LYS405 4.3 78.3 1.0 C A:LYS403 4.3 57.6 1.0 CE A:LYS403 4.4 63.6 1.0 CD A:LYS403 4.4 60.8 1.0 CB A:LYS403 4.7 54.7 1.0 C A:ARG402 4.8 54.0 1.0 CA A:LYS405 4.8 63.0 1.0 N A:LYS403 4.9 52.0 1.0

Iodine binding site 6 out of 14 in the Crystal Structure of CLK3 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of CLK3 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:54.7 occ:0.60 O A:HOH620 3.1 42.7 1.0 N A:LEU221 3.6 31.5 1.0 O A:HOH669 3.9 48.6 1.0 CA A:VAL220 3.9 27.6 1.0 NE A:ARG317 4.0 29.6 1.0 CD A:ARG317 4.1 27.7 1.0 CB A:GLU237 4.2 32.9 1.0 CG A:ARG317 4.3 25.5 1.0 C A:VAL220 4.3 28.6 1.0 CB A:LEU221 4.4 37.6 1.0 O A:CYS219 4.5 32.5 1.0 CA A:LEU221 4.5 32.9 1.0 CD2 A:LEU239 4.6 31.6 1.0 CD1 A:LEU239 4.7 28.8 1.0 CG A:LEU221 4.7 42.6 1.0 CB A:VAL220 4.8 28.1 1.0 N A:VAL220 4.8 27.5 1.0 CG1 A:VAL220 4.9 28.5 1.0 O A:LEU221 4.9 29.4 1.0 CB A:ARG317 5.0 24.2 1.0 C A:CYS219 5.0 29.6 1.0

Iodine binding site 7 out of 14 in the Crystal Structure of CLK3 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of CLK3 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:65.7 occ:0.65 O B:HOH601 3.3 56.0 1.0 NZ A:LYS209 3.5 44.5 1.0 O A:SER223 3.8 39.8 1.0 CA A:ASP224 3.9 37.1 1.0 N A:ASP224 3.9 37.4 1.0 C A:SER223 3.9 37.6 1.0 CE A:MET222 4.0 26.2 1.0 C1 B:EDO508 4.0 61.1 1.0 O A:MET222 4.3 31.8 1.0 CG A:MET222 4.3 30.7 1.0 C A:ASP224 4.4 35.0 1.0 CD1 A:TRP225 4.4 35.7 1.0 O1 B:EDO508 4.4 54.5 1.0 N A:TRP225 4.6 34.0 1.0 CA A:SER223 4.7 36.7 1.0 C A:MET222 4.8 33.5 1.0 SD A:MET222 4.8 30.1 1.0 CE A:LYS209 5.0 45.8 1.0

Iodine binding site 8 out of 14 in the Crystal Structure of CLK3 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of CLK3 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ B:I501 b:59.9 occ:0.85 ND2 B:ASN203 3.5 28.6 1.0 N A:ASN227 3.6 34.3 1.0 CD B:LYS207 3.9 40.4 1.0 CB A:PHE226 3.9 36.9 1.0 CA A:PHE226 4.0 35.1 1.0 CB B:LYS207 4.1 32.6 1.0 C A:PHE226 4.3 34.7 1.0 CA B:LYS207 4.4 30.1 1.0 OE1 B:GLU210 4.4 58.8 1.0 CB A:ASN227 4.5 39.5 1.0 N B:LYS207 4.5 30.2 1.0 CA A:ASN227 4.6 37.6 1.0 O A:ASN227 4.6 36.0 1.0 CG B:LYS207 4.6 36.3 1.0 O B:ASN203 4.6 29.5 1.0 CG B:ASN203 4.8 29.2 1.0 NZ B:LYS206 4.9 48.2 1.0

Iodine binding site 9 out of 14 in the Crystal Structure of CLK3 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of CLK3 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ B:I502 b:78.6 occ:0.90 O B:HOH717 3.0 44.7 1.0 OD1 B:ASP447 3.9 46.0 1.0 CG B:ASP447 4.0 45.8 1.0 CE1 B:HIS469 4.0 32.8 1.0 CG B:GLN444 4.0 45.4 1.0 O B:HOH790 4.0 58.1 1.0 CB B:ASP447 4.0 42.7 1.0 NE2 B:HIS469 4.3 33.4 1.0 CA B:GLN444 4.3 40.6 1.0 CB B:GLN444 4.5 42.1 1.0 NE2 B:GLN444 4.6 49.2 1.0 OD2 B:ASP447 4.6 47.6 1.0 CG B:PRO470 4.6 40.3 1.0 CB B:PRO470 4.8 40.4 1.0 CD B:GLN444 4.8 46.5 1.0 N B:GLN444 5.0 39.2 1.0

Iodine binding site 10 out of 14 in the Crystal Structure of CLK3 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of CLK3 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ B:I503 b:55.8 occ:0.60 O B:HOH721 2.8 43.6 1.0 O B:HOH738 3.5 49.1 1.0 N B:LEU221 3.7 32.1 1.0 CA B:VAL220 4.0 31.3 1.0 NE B:ARG317 4.0 27.9 1.0 CG B:ARG317 4.1 25.7 1.0 CD B:ARG317 4.1 27.0 1.0 C B:VAL220 4.4 31.5 1.0 CB B:GLU237 4.5 35.1 1.0 CB B:LEU221 4.6 37.5 1.0 O B:CYS219 4.6 33.2 1.0 CD2 B:LEU239 4.6 34.3 1.0 CB B:VAL220 4.7 32.5 1.0 CD1 B:LEU239 4.7 32.7 1.0 CA B:LEU221 4.7 34.4 1.0 CG1 B:VAL220 4.7 31.8 1.0 N B:VAL220 4.8 31.0 1.0 O B:LEU221 4.9 32.6 1.0 CG B:LEU221 5.0 42.8 1.0

A.Walter, A.Chaikuad, R.Helmer, N.Loaec, L.Preu, I.Ott, S.Knapp, L.Meijer, C.Kunick. Molecular Structures of CDC2-Like Kinases in Complex with A New Inhibitor Chemotype. Plos One V. 13 96761 2018.
ISSN: ESSN 1932-6203
PubMed: 29723265
DOI: 10.1371/JOURNAL.PONE.0196761