Chlorine in PDB 5k9d: Crystal Structure of Human Dihydroorotate Dehydrogenase at 1.7 A Resolution

All present enzymatic activity of Crystal Structure of Human Dihydroorotate Dehydrogenase at 1.7 A Resolution:
1.3.5.2;

The structure of Crystal Structure of Human Dihydroorotate Dehydrogenase at 1.7 A Resolution, PDB code: 5k9d was solved by T.A.Lewis, D.B.Sykes, J.M.Law, B.Munoz, D.T.Scadden, J.K.Rustiguel, M.C.Nonato, S.L.Schreiber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.57 / 1.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.140, 90.140, 122.152, 90.00, 90.00, 120.00
R / Rfree (%)	13.6 / 16

The binding sites of Chlorine atom in the Crystal Structure of Human Dihydroorotate Dehydrogenase at 1.7 A Resolution (pdb code 5k9d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Human Dihydroorotate Dehydrogenase at 1.7 A Resolution, PDB code: 5k9d:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Human Dihydroorotate Dehydrogenase at 1.7 A Resolution


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 Dihydroorotate Dehydrogenase at 1.7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:13.1 occ:0.97 HE22 A:GLN165 2.6 21.3 1.0 HB2 A:PRO204 3.1 10.9 1.0 O A:HOH672 3.2 14.1 1.0 HE1 A:HIS248 3.4 19.4 1.0 HB3 A:PRO204 3.4 10.9 1.0 NE2 A:GLN165 3.4 17.8 1.0 CE1 A:HIS248 3.5 16.2 1.0 O A:HOH831 3.6 37.5 1.0 CB A:PRO204 3.7 9.1 1.0 ND1 A:HIS248 3.7 14.4 1.0 HD1 A:HIS248 3.8 17.2 1.0 HE21 A:GLN165 3.9 21.3 1.0 NE2 A:HIS248 4.1 14.3 1.0 OE1 A:GLN165 4.2 15.5 1.0 HG A:LEU205 4.2 8.6 1.0 CD A:GLN165 4.2 15.8 1.0 O A:PRO204 4.3 8.9 1.0 HE2 A:HIS248 4.4 17.1 1.0 CG A:HIS248 4.5 14.1 1.0 HG2 A:PRO204 4.5 11.5 1.0 HD21 A:LEU205 4.6 16.1 1.0 HH21 A:ARG162 4.6 14.9 1.0 C A:PRO204 4.6 11.4 1.0 HE A:ARG162 4.7 10.9 1.0 CD2 A:HIS248 4.7 14.9 1.0 CG A:PRO204 4.7 9.6 1.0 CA A:PRO204 4.8 7.4 1.0 HD23 A:LEU205 4.9 16.1 1.0 CG A:LEU205 5.0 7.2 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Human Dihydroorotate Dehydrogenase at 1.7 A Resolution


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 Dihydroorotate Dehydrogenase at 1.7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl409 b:24.1 occ:0.85 HE22 A:GLN381 2.3 21.4 1.0 HH12 A:ARG347 2.3 23.1 0.6 HG3 A:GLN340 2.8 9.9 1.0 HD23 A:LEU343 2.9 18.5 1.0 O A:HOH535 3.0 18.7 0.9 O A:HOH558 3.1 21.2 1.0 NH1 A:ARG347 3.1 19.3 0.6 NE2 A:GLN381 3.1 17.8 1.0 HH11 A:ARG347 3.3 23.1 0.6 HD13 A:LEU377 3.3 18.7 1.0 HE21 A:GLN381 3.4 21.4 1.0 HA A:GLN340 3.5 9.0 1.0 HD22 A:LEU377 3.5 19.4 1.0 HB3 A:LEU343 3.6 10.7 1.0 CG A:GLN340 3.8 8.2 1.0 CD2 A:LEU343 3.9 15.4 1.0 HG3 A:GLU344 3.9 10.4 1.0 HH22 A:ARG347 4.0 9.4 0.6 HG A:LEU343 4.1 13.9 1.0 CD A:GLN381 4.2 16.4 1.0 CZ A:ARG347 4.2 23.1 0.6 HB2 A:GLN340 4.2 9.2 1.0 CD1 A:LEU377 4.2 15.6 1.0 HD21 A:LEU343 4.3 18.5 1.0 HG2 A:GLN340 4.3 9.9 1.0 CA A:GLN340 4.3 7.5 1.0 HB3 A:LEU377 4.3 12.1 1.0 CB A:GLN340 4.3 7.7 1.0 CG A:LEU343 4.4 11.6 1.0 CD2 A:LEU377 4.4 16.1 1.0 OE1 A:GLN381 4.4 18.2 1.0 CB A:LEU343 4.4 8.9 1.0 O A:GLN340 4.5 7.5 1.0 CD A:GLN340 4.5 10.4 1.0 HD11 A:LEU377 4.5 18.7 1.0 HD22 A:LEU343 4.5 18.5 1.0 HG2 A:GLU344 4.5 10.4 1.0 NH2 A:ARG347 4.5 7.8 0.6 OE1 A:GLN340 4.5 11.5 1.0 CG A:GLU344 4.7 8.7 1.0 HD21 A:LEU377 4.7 19.4 1.0 CG A:LEU377 4.8 12.6 1.0 HD3 A:ARG347 4.8 17.1 0.5 C A:GLN340 4.9 6.2 1.0 HD12 A:LEU377 4.9 18.7 1.0 HB2 A:LEU343 5.0 10.7 1.0 H A:GLU344 5.0 8.0 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Human Dihydroorotate Dehydrogenase at 1.7 A Resolution


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 Dihydroorotate Dehydrogenase at 1.7 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl410 b:14.8 occ:0.75 HH11 A:ARG245 2.5 12.8 1.0 NH1 A:ARG245 3.0 10.7 1.0 HH12 A:ARG245 3.1 12.8 1.0 HG2 A:ARG245 3.2 9.2 1.0 HD2 A:ARG245 3.8 11.2 1.0 CG A:ARG245 3.9 7.7 1.0 HG3 A:ARG245 4.1 9.2 1.0 CZ A:ARG245 4.1 11.7 1.0 CD A:ARG245 4.3 9.3 1.0 O A:HOH851 4.4 51.4 1.0 NE A:ARG245 4.6 10.9 1.0 O A:HOH791 4.6 26.8 0.7 O A:HOH691 5.0 20.8 1.0

T.A.Lewis, D.B.Sykes, J.M.Law, B.Munoz, J.K.Rustiguel, M.C.Nonato, D.T.Scadden, S.L.Schreiber. Development of ML390: A Human Dhodh Inhibitor That Induces Differentiation in Acute Myeloid Leukemia. Acs Med Chem Lett V. 7 1112 2016.
ISSN: ISSN 1948-5875
PubMed: 27994748
DOI: 10.1021/ACSMEDCHEMLETT.6B00316