SMTL ID : 5k9c.1

Crystal structure of human dihydroorotate dehydrogenase with ML390

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

1 x FNR: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL(Non-covalent)

FNR.1: 31 residues within 4Å: Chain A: H.28, A.67, A.68, G.69, K.72, G.91, S.92, V.106, V.115, N.117, Y.119, F.121, N.153, N.184, K.227, T.255, N.256, T.257, S.277, G.278, L.281, V.305, G.306, G.307, V.308, L.327, Y.328, T.329, A.330 Ligands: ORO.2, MLJ.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:N.117, A:Y.119, A:Y.328 Hydrogen bonds: A:A.68, A:K.72, A:S.92, A:S.92, A:N.153, A:K.227, A:T.255, A:N.256, A:N.256, A:G.278, A:G.307, A:Y.328, A:T.329, A:T.329 Water bridges: A:A.68, A:G.306, A:G.306, A:V.308, A:V.308

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 14 residues within 4Å: Chain A: K.72, N.117, R.118, Y.119, G.120, F.121, N.184, S.187, P.188, N.189, N.256, T.257, G.275 Ligands: FNR.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.121 Hydrogen bonds: A:N.117, A:N.117, A:Y.119, A:G.120, A:F.121, A:N.184, A:N.189, A:N.256, A:N.256, A:T.257 Salt bridges: A:K.72

1 x MLJ: ~{N}-[3-oxidanylidene-3-[[(1~{R})-1,2,3,4-tetrahydronaphthalen-1-yl]amino]propyl]-4-(trifluoromethyloxy)benzamide(Non-covalent)

MLJ.3: 19 residues within 4Å: Chain A: M.15, L.18, Q.19, L.22, P.24, A.27, H.28, L.30, A.31, F.34, F.70, V.106, R.108, V.115, Y.119, Y.328, T.332, F.333 Ligands: FNR.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.18, A:P.24, A:A.27, A:H.28, A:A.31, A:F.70, A:V.106, A:R.108, A:V.115, A:T.332, A:F.333 Hydrogen bonds: A:R.108, A:R.108, A:T.332, A:T.332

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: R.217, V.219, H.220 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.217, A:H.220 SO4.5: 2 residues within 4Å: Chain A: R.218, R.221 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.218 Water bridges: A:R.218, A:R.218, A:R.221 Salt bridges: A:R.221

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 8 residues within 4Å: Chain A: H.58, Q.140, A.141, T.144, L.150, L.177, A.178, D.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.179 Water bridges: A:D.179 ACT.7: 5 residues within 4Å: Chain A: D.283, T.286, Q.287, R.290, E.316 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.286 Water bridges: A:Q.287 Salt bridges: A:R.290 ACT.8: 2 residues within 4Å: Chain A: V.128, R.132 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.132 Water bridges: A:E.75, A:R.132 Salt bridges: A:R.132

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 3 residues within 4Å: Chain A: Q.137, P.176, H.220 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: Q.312, L.315, E.316, L.349, Q.353 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 3 residues within 4Å: Chain A: K.199, A.200, R.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.199, A:R.203, A:R.203 Water bridges: A:S.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lewis, T.A. et al., Development of ML390: A Human DHODH Inhibitor That Induces Differentiation in Acute Myeloid Leukemia. ACS Med Chem Lett (2016)

Release Date

2016-10-12

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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