Chlorine in PDB 3ur4: Crystal Structure of Human Wd Repeat Domain 5 with Compound

The structure of Crystal Structure of Human Wd Repeat Domain 5 with Compound, PDB code: 3ur4 was solved by A.Dong, L.Dombrovski, G.Senisterra, A.Wernimont, G.A.Wasney, A.Allalihassani, K.T.Nguyen, D.Smil, Y.Bolshan, T.Hajian, G.Poda, I.Chau, R.Al-Awar, C.Bountra, J.Weigelt, A.M.Edwards, C.H.Arrowsmith, P.Brown, M.Schapira, M.Vedadi, H.Wu, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.829, 47.002, 112.904, 90.00, 117.90, 90.00
R / Rfree (%)	18.2 / 21.3

The binding sites of Chlorine atom in the Crystal Structure of Human Wd Repeat Domain 5 with Compound (pdb code 3ur4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Human Wd Repeat Domain 5 with Compound, PDB code: 3ur4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Wd Repeat Domain 5 with Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1001 b:36.9 occ:1.00 O A:HOH700 2.9 26.4 1.0 CG A:ASN225 3.3 22.6 1.0 N A:ASN225 3.3 21.3 1.0 OD1 A:ASN225 3.3 22.4 1.0 CD A:PRO224 3.5 20.4 1.0 CB A:SER223 3.7 19.4 1.0 ND2 A:ASN225 3.7 23.2 1.0 N A:PRO224 3.7 20.2 1.0 CB A:ASN225 3.8 21.9 1.0 OG A:SER223 3.8 18.8 1.0 CB A:PRO224 3.9 20.8 1.0 CG A:PRO224 4.0 20.9 1.0 CA A:ASN225 4.1 21.7 1.0 CA A:PRO224 4.2 20.7 1.0 C A:PRO224 4.2 20.9 1.0 O A:HOH518 4.2 23.8 1.0 C A:SER223 4.2 19.6 1.0 CA A:SER223 4.5 19.4 1.0 O A:HOH701 4.6 26.9 1.0 CD2 A:TYR228 4.6 23.7 1.0 CE2 A:TYR228 4.8 24.6 1.0 UNK A:UNX1022 4.9 30.0 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Wd Repeat Domain 5 with Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1002 b:32.5 occ:1.00 O A:HOH428 2.9 31.2 1.0 ND2 A:ASN265 2.9 20.1 1.0 N A:CYS309 2.9 14.9 1.0 O A:HOH368 2.9 21.8 1.0 O A:HOH583 3.5 23.3 1.0 O A:HOH8 3.6 11.4 1.0 O A:CYS309 3.6 14.9 1.0 NZ A:LYS221 3.7 27.5 1.0 CA A:ALA308 3.7 14.5 1.0 CG A:ASN265 3.7 18.7 1.0 C A:ALA308 3.8 14.6 1.0 CA A:CYS309 3.8 15.1 1.0 CB A:CYS309 4.0 15.1 1.0 O4 A:SO43000 4.1 39.6 0.7 CB A:ALA308 4.1 14.4 1.0 CB A:ASN265 4.1 18.0 1.0 C A:CYS309 4.1 14.8 1.0 O A:HOH436 4.2 20.0 1.0 O A:HOH678 4.4 25.0 1.0 O3 A:SO43000 4.6 39.6 0.7 OD1 A:ASN265 4.6 22.7 1.0 SG A:CYS309 4.6 16.6 1.0 S A:SO43000 4.8 38.9 0.7 O A:THR307 4.9 13.8 1.0 N A:ALA308 5.0 14.3 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Wd Repeat Domain 5 with Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1003 b:35.0 occ:1.00 O A:HOH634 2.6 28.5 1.0 O A:SER184 2.8 15.4 1.0 O A:HOH626 3.0 26.6 1.0 N A:ALA201 3.0 16.3 1.0 OD1 A:ASP199 3.2 19.5 1.0 N A:THR200 3.4 16.2 1.0 CB A:ALA201 3.5 17.0 1.0 C A:SER184 3.6 15.1 1.0 CA A:SER184 3.6 15.1 1.0 CB A:THR200 3.7 15.9 1.0 CG A:ASP199 3.8 17.6 1.0 CA A:ALA201 3.8 16.9 1.0 CA A:THR200 3.8 16.0 1.0 C A:THR200 3.9 16.2 1.0 CB A:SER184 3.9 15.1 1.0 OD2 A:ASP199 4.1 18.4 1.0 O A:HOH385 4.2 37.0 1.0 C A:ASP199 4.2 16.4 1.0 O A:HOH503 4.3 52.5 1.0 O A:HOH521 4.4 27.9 1.0 OG1 A:THR200 4.5 15.3 1.0 CA A:ASP199 4.6 16.7 1.0 CB A:ASP199 4.8 16.9 1.0 CG2 A:THR200 4.8 15.3 1.0 O A:GLY183 4.9 14.6 1.0 N A:LEU185 4.9 14.8 1.0 N A:SER184 4.9 15.1 1.0 O A:ASP199 5.0 16.4 1.0 O A:HOH478 5.0 24.1 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Wd Repeat Domain 5 with Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1005 b:37.8 occ:1.00 O A:HOH688 2.6 32.0 1.0 O A:GLY226 2.8 21.1 1.0 ND2 A:ASN180 2.9 14.4 1.0 O A:HOH407 3.0 32.4 1.0 C A:GLY226 3.5 21.4 1.0 CA A:GLY226 3.6 21.2 1.0 CD1 A:LEU185 3.7 16.0 1.0 CB A:ASN180 3.8 14.3 1.0 CG A:ASN180 3.8 14.4 1.0 O A:HOH614 4.2 27.1 1.0 CE1 A:PHE222 4.3 18.4 1.0 N A:LYS227 4.6 21.6 1.0 CG A:LEU185 4.6 15.1 1.0 CD1 A:PHE222 4.6 18.1 1.0 O A:ASN225 4.9 21.6 1.0 CD2 A:TYR243 4.9 26.1 1.0 N A:GLY226 4.9 21.4 1.0 CZ A:PHE222 4.9 18.6 1.0 O A:HOH621 5.0 28.7 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human Wd Repeat Domain 5 with Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl335 b:30.6 occ:1.00 O B:HOH418 2.8 28.0 1.0 N B:ASP98 3.1 14.6 1.0 CG B:ASP98 3.3 15.8 1.0 OD1 B:ASP98 3.4 16.4 1.0 CB B:SER141 3.4 14.8 1.0 N B:SER97 3.5 13.2 1.0 CB B:ASP98 3.6 15.1 1.0 OG B:SER141 3.6 13.6 1.0 OD2 B:ASP98 3.8 18.0 1.0 CB B:SER97 3.9 13.5 1.0 CB B:SER96 3.9 12.4 1.0 CA B:SER97 3.9 13.9 1.0 C B:SER97 4.0 14.1 1.0 CA B:ASP98 4.0 14.8 1.0 OG B:SER96 4.0 11.9 1.0 C B:SER96 4.2 13.1 1.0 O B:GLN140 4.3 14.8 1.0 O B:HOH491 4.4 23.8 1.0 CA B:SER96 4.6 12.7 1.0 CA B:SER141 4.8 14.9 1.0 O2 B:EDO2001 4.8 29.1 0.8 OG B:SER97 4.8 14.0 1.0 C B:GLN140 5.0 14.9 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of Human Wd Repeat Domain 5 with Compound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human Wd Repeat Domain 5 with Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1004 b:28.0 occ:1.00 OD2 B:ASP92 2.6 12.4 1.0 O B:HOH22 2.9 13.4 1.0 O B:CYS135 2.9 11.9 1.0 NZ B:LYS52 3.1 13.3 1.0 ND2 B:ASN136 3.3 12.6 1.0 CG B:ASP92 3.5 13.1 1.0 OD1 B:ASP92 3.7 12.7 1.0 O B:HOH515 3.7 35.1 1.0 CE2 B:PHE263 3.8 20.1 1.0 CG B:ASN136 3.9 13.0 1.0 CZ B:PHE263 3.9 19.9 1.0 C B:CYS135 4.0 11.5 1.0 OD1 B:ASN136 4.1 13.4 1.0 N B:CYS135 4.1 11.4 1.0 CE B:LYS52 4.2 12.8 1.0 O B:HOH365 4.2 15.0 1.0 O B:HOH554 4.2 14.8 1.0 O B:VAL177 4.3 12.2 1.0 O B:HOH357 4.6 15.0 1.0 CA B:CYS135 4.7 11.5 1.0 O B:VAL93 4.8 12.2 0.5 O B:VAL93 4.8 12.3 0.5 CB B:ASN136 4.8 12.1 1.0 CB B:CYS134 4.9 11.8 1.0 CB B:ASP92 5.0 12.1 1.0 N B:ASN136 5.0 11.6 1.0

G.Senisterra, H.Wu, A.Allali-Hassani, G.A.Wasney, D.Barsyte-Lovejoy, L.Dombrovski, A.Dong, K.T.Nguyen, D.Smil, Y.Bolshan, T.Hajian, H.He, A.Seitova, I.Chau, F.Li, G.Poda, J.F.Couture, P.J.Brown, R.Al-Awar, M.Schapira, C.H.Arrowsmith, M.Vedadi. Small-Molecule Inhibition of Mll Activity By Disruption of Its Interaction with WDR5. Biochem. J. V. 449 151 2013.
ISSN: ESSN 1470-8728
PubMed: 22989411
DOI: 10.1042/BJ20121280