Chlorine in PDB 6gim: Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18)

The structure of Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18), PDB code: 6gim was solved by C.R.Millan, C.Dardonvile, H.P.De Koning, N.Saperas, J.L.Campos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.04 / 1.43
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	22.630, 40.470, 72.255, 90.00, 93.91, 90.00
R / Rfree (%)	14.3 / 19.3

The structure of Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18) also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Chlorine atom in the Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18) (pdb code 6gim). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18), PDB code: 6gim:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl101 b:33.4 occ:0.50 CL1 D:EZK101 0.0 33.4 0.5 C15 D:EZK101 1.7 25.8 0.5 C14 D:EZK101 2.7 20.8 0.5 C16 D:EZK101 2.7 26.5 0.5 N4 D:EZK101 2.9 20.1 0.5 O D:HOH207 3.1 38.6 1.0 C5' D:DT6 3.7 20.4 1.0 C13 D:EZK101 4.0 20.7 0.5 C11 D:EZK101 4.0 23.1 0.5 O3' D:DT5 4.2 19.3 1.0 C17 D:EZK101 4.2 19.6 0.5 OP1 D:DT6 4.2 26.2 1.0 C12 D:EZK101 4.5 19.6 0.5 C4' D:DT6 4.6 19.1 1.0 O5' D:DT6 4.7 20.7 1.0 P D:DT6 4.7 21.1 1.0 O1 D:EZK101 4.8 24.6 0.5 N6 D:EZK101 5.0 21.1 0.5

Chlorine binding site 2 out of 3 in the Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl101 b:20.9 occ:0.50 CL1 C:EZK101 0.0 20.9 0.5 C15 C:EZK101 1.7 17.5 0.5 C16 C:EZK101 2.7 14.0 0.5 C14 C:EZK101 2.7 14.8 0.5 N4 C:EZK101 3.0 13.4 0.5 O C:HOH214 3.3 30.9 1.0 C11 C:EZK101 4.0 14.6 0.5 C13 C:EZK101 4.0 15.1 0.5 C17 C:EZK101 4.3 11.9 0.5 C12 C:EZK101 4.5 14.9 0.5 O1 C:EZK101 4.8 20.1 0.5

Chlorine binding site 3 out of 3 in the Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Dna Duplex D(Aaattt)2 with [N-(3-Chloro-4-((4,5- Dihydro-1H-Imidazol-2-Yl)Amino)Phenyl)-4-((4,5-Dihydro-1H-Imidazol-2- Yl)Amino)Benzamide] - (Drug JNI18) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl101 b:24.6 occ:1.00 CL1 B:EZK101 0.0 24.6 1.0 C15 B:EZK101 1.7 15.1 1.0 C16 B:EZK101 2.6 15.4 1.0 C14 B:EZK101 2.7 12.0 1.0 N4 B:EZK101 3.0 12.4 1.0 O B:HOH207 3.2 27.1 1.0 C4' A:DT4 3.6 17.4 1.0 O3' A:DT4 3.7 19.6 1.0 C5' A:DT4 3.8 14.7 1.0 C11 B:EZK101 3.9 12.5 1.0 C13 B:EZK101 4.0 11.9 1.0 C17 B:EZK101 4.2 11.3 1.0 C3' A:DT4 4.4 16.2 1.0 C12 B:EZK101 4.4 11.3 1.0 O4' A:DT4 4.6 13.4 1.0 OP1 A:DT5 4.7 34.4 1.0 P A:DT5 4.9 23.8 1.0 O1 B:EZK101 4.9 16.7 1.0

C.R.Millan, F.J.Acosta-Reyes, L.Lagartera, G.U.Ebiloma, L.Lemgruber, J.J.Nue Martinez, N.Saperas, C.Dardonville, H.P.De Koning, J.L.Campos. Functional and Structural Analysis of at-Specific Minor Groove Binders That Disrupt Dna-Protein Interactions and Cause Disintegration of the Trypanosoma Brucei Kinetoplast. Nucleic Acids Res. V. 45 8378 2017.
ISSN: ESSN 1362-4962
PubMed: 28637278
DOI: 10.1093/NAR/GKX521