Chlorine in PDB 5k9c: Crystal Structure of Human Dihydroorotate Dehydrogenase with ML390

All present enzymatic activity of Crystal Structure of Human Dihydroorotate Dehydrogenase with ML390:
1.3.5.2;

The structure of Crystal Structure of Human Dihydroorotate Dehydrogenase with ML390, PDB code: 5k9c 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)	25.95 / 1.66
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.900, 89.900, 121.771, 90.00, 90.00, 120.00
R / Rfree (%)	13.1 / 15

The structure of Crystal Structure of Human Dihydroorotate Dehydrogenase with ML390 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Chlorine atom in the Crystal Structure of Human Dihydroorotate Dehydrogenase with ML390 (pdb code 5k9c). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Human Dihydroorotate Dehydrogenase with ML390, PDB code: 5k9c:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Human Dihydroorotate Dehydrogenase with ML390


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 with ML390 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:13.6 occ:0.78 HE22 A:GLN165 2.6 30.2 1.0 O A:HOH659 3.1 18.4 1.0 HB2 A:PRO204 3.2 15.8 1.0 HB3 A:PRO204 3.4 15.8 1.0 HE1 A:HIS248 3.4 23.8 1.0 NE2 A:GLN165 3.5 25.2 1.0 CE1 A:HIS248 3.5 19.8 1.0 O A:HOH773 3.6 47.9 1.0 CB A:PRO204 3.7 13.2 1.0 ND1 A:HIS248 3.8 18.3 1.0 HD1 A:HIS248 3.8 22.0 1.0 HE21 A:GLN165 4.0 30.2 1.0 NE2 A:HIS248 4.2 21.8 1.0 OE1 A:GLN165 4.2 23.9 1.0 HG A:LEU205 4.2 15.6 1.0 CD A:GLN165 4.3 20.3 1.0 O A:PRO204 4.3 13.7 1.0 HE2 A:HIS248 4.5 26.1 1.0 CG A:HIS248 4.5 18.1 1.0 HG2 A:PRO204 4.6 19.2 1.0 HD21 A:LEU205 4.6 23.2 1.0 HH21 A:ARG162 4.6 20.9 1.0 HE A:ARG162 4.7 14.9 1.0 C A:PRO204 4.7 11.9 1.0 CD2 A:HIS248 4.7 19.3 1.0 CG A:PRO204 4.7 16.0 1.0 CA A:PRO204 4.8 10.8 1.0 HD23 A:LEU205 4.9 23.2 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Human Dihydroorotate Dehydrogenase with ML390


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 with ML390 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl409 b:26.6 occ:0.70 HH12 A:ARG347 2.3 32.0 0.5 HE22 A:GLN381 2.3 31.0 1.0 HG3 A:GLN340 2.8 14.2 1.0 HD23 A:LEU343 3.0 22.2 1.0 O A:HOH523 3.0 25.8 1.0 NH1 A:ARG347 3.1 26.6 0.5 NE2 A:GLN381 3.1 25.9 1.0 O A:HOH541 3.2 27.8 0.9 HD13 A:LEU377 3.3 23.6 1.0 HH11 A:ARG347 3.4 32.0 0.5 HE21 A:GLN381 3.4 31.0 1.0 HA A:GLN340 3.5 12.8 1.0 HD22 A:LEU377 3.6 25.0 1.0 HB3 A:LEU343 3.6 15.4 1.0 CG A:GLN340 3.8 11.8 1.0 HH22 A:ARG347 4.0 16.1 0.5 CD2 A:LEU343 4.0 18.5 1.0 HG3 A:GLU344 4.0 13.7 1.0 CD1 A:LEU377 4.2 19.7 1.0 HB2 A:GLN340 4.2 14.9 1.0 HG A:LEU343 4.2 16.4 1.0 CD A:GLN381 4.2 23.2 1.0 CZ A:ARG347 4.2 26.8 0.5 HG2 A:GLN340 4.3 14.2 1.0 CA A:GLN340 4.3 10.7 1.0 CB A:GLN340 4.3 12.4 1.0 HB3 A:LEU377 4.3 17.4 1.0 HD11 A:LEU377 4.4 23.6 1.0 HD21 A:LEU343 4.4 22.2 1.0 CD2 A:LEU377 4.4 20.8 1.0 OE1 A:GLN381 4.4 28.2 1.0 HG2 A:GLU344 4.5 13.7 1.0 CD A:GLN340 4.5 13.1 1.0 CB A:LEU343 4.5 12.8 1.0 NH2 A:ARG347 4.5 13.4 0.5 CG A:LEU343 4.5 13.7 1.0 O A:GLN340 4.5 11.9 1.0 HD22 A:LEU343 4.5 22.2 1.0 OE1 A:GLN340 4.6 14.7 1.0 HD21 A:LEU377 4.6 25.0 1.0 CG A:GLU344 4.7 11.4 1.0 CG A:LEU377 4.8 16.4 1.0 HD12 A:LEU377 4.8 23.6 1.0 HD3 A:ARG347 4.9 18.9 0.5 C A:GLN340 4.9 11.7 1.0 HB2 A:LEU343 4.9 15.4 1.0 O A:HOH719 5.0 23.2 0.8

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