Chlorine in PDB 3rlr: Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile

The structure of Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile, PDB code: 3rlr was solved by P.-P.Kung, P.-J.Sinnema, P.Richardson, M.J.Hickey, K.S.Gajiwala, F.Wang, B.Huang, G.Mcclellan, J.Wang, K.Maegley, S.Bergqvist, P.P.Mehta, R.Kania, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.55 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.051, 79.131, 117.950, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 20.9

The binding sites of Chlorine atom in the Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile (pdb code 3rlr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile, PDB code: 3rlr:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl901 b:13.3 occ:1.00 CL2 A:3RR901 0.0 13.3 1.0 C9 A:3RR901 1.7 11.1 1.0 C10 A:3RR901 2.7 12.6 1.0 C8 A:3RR901 2.8 11.2 1.0 C2 A:3RR901 3.2 11.7 1.0 C4 A:3RR901 3.4 13.8 1.0 C15 A:3RR901 3.4 14.2 1.0 C5 A:3RR901 3.6 13.0 1.0 N4 A:3RR901 3.8 13.9 1.0 CE A:MET98 3.8 15.0 1.0 CD2 A:LEU107 3.8 17.2 1.0 CD1 A:PHE138 3.9 12.0 1.0 CG1 A:VAL150 4.0 12.3 1.0 CE1 A:PHE138 4.0 13.0 1.0 C11 A:3RR901 4.0 13.8 1.0 C13 A:3RR901 4.1 11.5 1.0 N2 A:3RR901 4.1 12.0 1.0 CG2 A:VAL150 4.2 13.2 1.0 CD1 A:LEU107 4.2 17.1 1.0 CG2 A:VAL186 4.3 13.2 1.0 CG A:LEU107 4.4 16.6 1.0 C3 A:3RR901 4.5 12.1 1.0 CG A:PHE138 4.5 11.9 1.0 CG2 A:THR184 4.6 14.1 1.0 C12 A:3RR901 4.6 13.3 1.0 C6 A:3RR901 4.7 12.5 1.0 CZ A:PHE138 4.7 11.8 1.0 CB A:VAL150 4.7 11.2 1.0 SD A:MET98 4.8 16.0 1.0 C1 A:3RR901 5.0 13.7 1.0

Chlorine binding site 2 out of 4 in the Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl901 b:15.8 occ:1.00 CL1 A:3RR901 0.0 15.8 1.0 C11 A:3RR901 1.7 13.8 1.0 C10 A:3RR901 2.7 12.6 1.0 C12 A:3RR901 2.8 13.3 1.0 O1 A:3RR901 3.0 17.4 1.0 CB A:PHE138 3.5 9.9 1.0 O A:HOH4 3.6 12.0 1.0 O A:ASN106 3.7 20.4 1.0 O A:HOH251 3.8 24.7 1.0 CD2 A:PHE138 3.9 12.2 1.0 O A:HOH324 3.9 28.1 1.0 CE2 A:TYR139 4.0 13.8 1.0 CG A:PHE138 4.0 11.9 1.0 C9 A:3RR901 4.0 11.1 1.0 C13 A:3RR901 4.1 11.5 1.0 C14 A:3RR901 4.4 19.6 1.0 CZ A:TYR139 4.4 15.8 1.0 OH A:TYR139 4.4 17.7 1.0 CG A:LEU107 4.4 16.6 1.0 CD1 A:LEU107 4.5 17.1 1.0 C8 A:3RR901 4.6 11.2 1.0 CD2 A:TYR139 4.6 13.9 1.0 O A:GLY135 4.6 17.1 1.0 C A:ASN106 4.8 21.9 1.0 CA A:PHE138 4.9 11.6 1.0 CE2 A:PHE138 4.9 11.7 1.0 CA A:LEU107 5.0 19.2 1.0 CD1 A:PHE138 5.0 12.0 1.0

Chlorine binding site 3 out of 4 in the Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl901 b:14.8 occ:1.00 CL2 B:3RR901 0.0 14.8 1.0 C9 B:3RR901 1.7 14.7 1.0 C10 B:3RR901 2.7 13.7 1.0 C8 B:3RR901 2.8 14.7 1.0 C2 B:3RR901 3.2 14.3 1.0 C4 B:3RR901 3.4 14.2 1.0 C15 B:3RR901 3.4 14.7 1.0 C5 B:3RR901 3.6 13.6 1.0 CE B:MET98 3.7 15.0 1.0 CD2 B:LEU107 3.7 14.4 1.0 N4 B:3RR901 3.7 15.7 1.0 CG1 B:VAL150 4.0 13.8 1.0 CD1 B:PHE138 4.0 14.3 1.0 C11 B:3RR901 4.0 15.0 1.0 CE1 B:PHE138 4.1 16.1 1.0 C13 B:3RR901 4.1 13.4 1.0 N2 B:3RR901 4.1 14.1 1.0 CG2 B:VAL150 4.3 14.1 1.0 CD1 B:LEU107 4.3 16.6 1.0 CG B:LEU107 4.3 16.5 1.0 CG2 B:VAL186 4.4 13.9 1.0 C3 B:3RR901 4.5 14.5 1.0 CG2 B:THR184 4.5 14.4 1.0 C12 B:3RR901 4.6 15.5 1.0 CG B:PHE138 4.6 12.8 1.0 C6 B:3RR901 4.7 14.3 1.0 SD B:MET98 4.7 16.3 1.0 CZ B:PHE138 4.7 15.6 1.0 CB B:VAL150 4.8 12.5 1.0 C1 B:3RR901 5.0 12.9 1.0

Chlorine binding site 4 out of 4 in the Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Co-Crystal Structure of the HSP90 Atp Binding Domain in Complex with 4-(2,4-Dichloro-5-Methoxyphenyl)-2,6-Dimethyl-7H-Pyrrolo[2,3- D]Pyrimidine-5-Carbonitrile within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl901 b:17.8 occ:1.00 CL1 B:3RR901 0.0 17.8 1.0 C11 B:3RR901 1.7 15.0 1.0 C10 B:3RR901 2.7 13.7 1.0 C12 B:3RR901 2.8 15.5 1.0 O1 B:3RR901 3.0 15.9 1.0 CB B:PHE138 3.5 12.0 1.0 O B:ASN106 3.5 17.3 1.0 O B:HOH7 3.6 16.2 1.0 O B:HOH291 3.9 25.5 1.0 CD2 B:PHE138 3.9 13.6 1.0 O B:HOH320 3.9 27.0 1.0 CG B:PHE138 3.9 12.8 1.0 C9 B:3RR901 4.0 14.7 1.0 C13 B:3RR901 4.1 13.4 1.0 CE2 B:TYR139 4.1 16.5 1.0 CG B:LEU107 4.4 16.5 1.0 C14 B:3RR901 4.4 19.4 1.0 O B:GLY135 4.5 21.0 1.0 OH B:TYR139 4.5 18.6 1.0 CZ B:TYR139 4.5 16.2 1.0 CD1 B:LEU107 4.6 16.6 1.0 C8 B:3RR901 4.6 14.7 1.0 C B:ASN106 4.6 18.2 1.0 CD2 B:TYR139 4.7 16.0 1.0 CA B:LEU107 4.8 16.8 1.0 CA B:PHE138 4.8 12.9 1.0 O B:HOH358 4.9 25.7 1.0 CE2 B:PHE138 4.9 14.8 1.0 N B:PHE138 5.0 13.3 1.0 CD1 B:PHE138 5.0 14.3 1.0

P.P.Kung, P.J.Sinnema, P.Richardson, M.J.Hickey, K.S.Gajiwala, F.Wang, B.Huang, G.Mcclellan, J.Wang, K.Maegley, S.Bergqvist, P.P.Mehta, R.Kania. Design Strategies to Target Crystallographic Waters Applied to the HSP90 Molecular Chaperone. Bioorg.Med.Chem.Lett. V. 21 3557 2011.
ISSN: ISSN 0960-894X
PubMed: 21612924
DOI: 10.1016/J.BMCL.2011.04.130