Iodine in PDB 8r8e: DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile

All present enzymatic activity of DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile:
2.7.12.1;

The structure of DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile, PDB code: 8r8e was solved by J.Stahlecker, M.Dammann, T.Stehle, F.M.Boeckler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.08 / 2.22
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	244.236, 64.473, 147.332, 90, 115.58, 90
R / Rfree (%)	19.9 / 23.4

The binding sites of Iodine atom in the DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile (pdb code 8r8e). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile, PDB code: 8r8e:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:78.9 occ:1.00 I1 A:YOX501 0.0 78.9 1.0 C4 A:YOX501 2.1 42.2 1.0 C3 A:YOX501 3.0 39.6 1.0 C5 A:YOX501 3.1 45.0 1.0 O A:HOH618 3.3 61.3 1.0 N1 A:YOX501 3.6 42.0 1.0 CD2 A:LEU294 3.7 40.9 1.0 CD1 A:ILE165 3.8 53.5 1.0 O A:LEU241 3.9 57.3 1.0 O A:HOH761 3.9 43.8 1.0 N A:LEU241 4.0 51.6 1.0 CE A:MET240 4.1 64.2 1.0 CB A:ALA186 4.2 42.6 1.0 CB A:LEU241 4.3 46.5 1.0 C A:LEU241 4.3 52.5 1.0 C2 A:YOX501 4.4 41.4 1.0 C6 A:YOX501 4.4 41.4 1.0 CA A:LEU241 4.4 50.4 1.0 CG1 A:ILE165 4.7 56.6 1.0 CG1 A:VAL173 4.8 45.7 1.0 O A:SER242 4.9 53.0 1.0 SD A:MET240 4.9 67.7 1.0 C7 A:YOX501 4.9 44.4 1.0 C1 A:YOX501 4.9 41.9 1.0

Iodine binding site 2 out of 4 in the DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile within 5.0Å range: probe atom residue distance (Å) B Occ B:I502 b:85.4 occ:1.00 I1 B:YOX502 0.0 85.4 1.0 C4 B:YOX502 2.1 58.8 1.0 C3 B:YOX502 3.0 53.5 1.0 C5 B:YOX502 3.1 53.7 1.0 N1 B:YOX502 3.5 57.9 1.0 CD2 B:LEU294 3.7 51.3 1.0 O B:LEU241 3.8 61.9 1.0 O B:HOH724 3.9 51.2 1.0 CE B:MET240 4.0 59.9 1.0 CD1 B:ILE165 4.1 65.7 1.0 N B:LEU241 4.1 60.6 1.0 CB B:ALA186 4.2 51.4 1.0 C B:LEU241 4.3 61.9 1.0 CB B:LEU241 4.3 52.6 1.0 C2 B:YOX502 4.4 50.5 1.0 C6 B:YOX502 4.4 53.8 1.0 CA B:LEU241 4.4 61.0 1.0 CG1 B:VAL173 4.7 54.5 1.0 O B:SER242 4.8 59.1 1.0 C7 B:YOX502 4.9 58.7 1.0 CG1 B:ILE165 4.9 69.7 1.0 C1 B:YOX502 4.9 50.2 1.0 SD B:MET240 4.9 74.5 1.0

Iodine binding site 3 out of 4 in the DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile within 5.0Å range: probe atom residue distance (Å) B Occ C:I502 b:207.4 occ:1.00 I1 C:YOX502 0.0 207.4 1.0 C4 C:YOX502 2.1 76.3 1.0 C3 C:YOX502 3.0 79.5 1.0 C5 C:YOX502 3.1 72.5 1.0 N1 C:YOX502 3.5 74.7 1.0 CD2 C:LEU294 3.6 68.8 1.0 O C:LEU241 3.8 89.6 1.0 O C:HOH656 3.9 67.5 1.0 N C:LEU241 4.1 88.5 1.0 CE C:MET240 4.1 99.6 1.0 C C:LEU241 4.3 89.1 1.0 CB C:LEU241 4.3 80.6 1.0 CG2 C:ILE165 4.4 105.7 1.0 C2 C:YOX502 4.4 74.4 1.0 C6 C:YOX502 4.4 70.7 1.0 CA C:LEU241 4.4 89.8 1.0 CB C:ALA186 4.5 81.8 1.0 O C:SER242 4.6 87.3 1.0 C7 C:YOX502 4.9 69.7 1.0 SD C:MET240 4.9 98.0 1.0 C1 C:YOX502 4.9 65.7 1.0

Iodine binding site 4 out of 4 in the DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of DYRK1A in Complex with 2-Cyclopentyl-7-Iodo-1H-Indole-3-Carbonitrile within 5.0Å range: probe atom residue distance (Å) B Occ D:I501 b:94.5 occ:1.00 I1 D:YOX501 0.0 94.5 1.0 C4 D:YOX501 2.1 73.5 1.0 C3 D:YOX501 3.0 69.0 1.0 C5 D:YOX501 3.1 69.5 1.0 N1 D:YOX501 3.5 67.8 1.0 CD2 D:LEU294 3.7 63.1 1.0 O D:HOH662 3.7 61.0 1.0 O D:LEU241 3.8 75.3 1.0 CE D:MET240 3.9 85.1 1.0 CB D:ALA186 4.1 66.4 1.0 N D:LEU241 4.1 67.0 1.0 CG2 D:ILE165 4.2 75.1 1.0 CB D:LEU241 4.2 61.9 1.0 C D:LEU241 4.3 68.8 1.0 C2 D:YOX501 4.4 67.9 1.0 C6 D:YOX501 4.4 73.8 1.0 CA D:LEU241 4.4 62.1 1.0 CG1 D:VAL173 4.6 69.4 1.0 O D:SER242 4.8 58.3 1.0 C7 D:YOX501 4.9 73.4 1.0 C1 D:YOX501 4.9 69.0 1.0 SD D:MET240 4.9 80.6 1.0

M.U.Engelhardt, M.O.Zimmermann, M.Dammann, J.Stahlecker, A.Poso, T.Kronenberger, C.Kunick, T.Stehle, F.M.Boeckler. Halogen Bonding on Water─A Drop in the Ocean? J Chem Theory Comput 2024.
ISSN: ISSN 1549-9626
PubMed: 39291905
DOI: 10.1021/ACS.JCTC.4C00834