SMTL ID : 9dhi.1

DHODH in complex with Compound 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 25 residues within 4Å: Chain A: A.68, A.69, G.70, K.73, G.92, S.93, N.118, Y.120, N.154, N.185, K.228, T.256, N.257, T.258, S.278, G.279, L.282, V.306, G.307, G.308, L.328, Y.329, T.330 Ligands: ORO.2, 01.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:N.118, A:Y.120, A:Y.329, A:Y.329 Hydrogen bonds: A:A.69, A:K.73, A:S.93, A:S.93, A:N.154, A:K.228, A:K.228, A:N.257, A:G.279, A:G.308, A:Y.329, A:T.330, A:T.330 Water bridges: A:A.69, A:G.307, A:V.309

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 13 residues within 4Å: Chain A: K.73, N.118, R.119, Y.120, G.121, F.122, N.185, S.188, P.189, N.190, N.257, T.258 Ligands: FMN.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.122 Hydrogen bonds: A:N.118, A:N.118, A:N.118, A:Y.120, A:G.121, A:F.122, A:N.185, A:N.190, A:N.257, A:N.257 Water bridges: A:S.188, A:S.188 Salt bridges: A:K.73

1 x 01: (2M,6P)-6-[4-ethyl-3-(hydroxymethyl)-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl]-7-fluoro-2-(2-methylphenyl)-4-(propan-2-yl)phthalazin-1(2H)-one

01.3: 23 residues within 4Å: Chain A: Y.11, M.16, L.19, Q.20, L.23, P.25, A.28, H.29, A.32, F.35, T.36, L.40, L.41, F.71, V.107, R.109, V.116, Y.329, L.332, T.333, P.337 Ligands: FMN.1, PGE.25 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.11, A:L.19, A:L.23, A:A.32, A:F.35, A:F.35, A:L.41, A:V.107, A:L.332, A:T.333, A:P.337 Hydrogen bonds: A:Q.20 Water bridges: A:T.333 pi-Stacking: A:F.35

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

SO4.4: 3 residues within 4Å: Chain A: R.218, V.220, H.221 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.218, A:H.221 SO4.5: 2 residues within 4Å: Chain A: R.219, R.222 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.219, A:R.222 Salt bridges: A:R.219, A:R.222 SO4.15: 8 residues within 4Å: Chain A: E.26, H.29, R.30, K.73, H.74, Y.120, N.123 Ligands: EDO.22 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.123 Salt bridges: A:H.29, A:R.30, A:H.74

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

ACT.6: 6 residues within 4Å: Chain A: Q.141, A.142, T.145, L.178, A.179, D.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.145, A:D.180 Water bridges: A:E.146 ACT.21: 4 residues within 4Å: Chain A: D.284, T.287, Q.288, R.291 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.284, A:Q.288 Salt bridges: A:R.291 ACT.24: 6 residues within 4Å: Chain A: H.59, A.179, D.180, R.219, V.220, R.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.222, A:R.222 Salt bridges: A:H.59 ACT.29: 3 residues within 4Å: Chain A: T.234, Q.236, D.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.237

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

CL.7: 2 residues within 4Å: Chain A: S.261, R.262 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: P.25, F.108, R.109, L.270 Ligands: EDO.27 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: Q.138, P.177, H.221 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: S.128, H.132 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: T.234, S.235 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: R.262, T.274, G.275 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: V.56, L.57, G.58 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: R.214, D.215 Ligand excluded by PLIP

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.16: 2 residues within 4Å: Chain A: G.21, L.22 No protein-ligand interaction detected (PLIP) EDO.17: 4 residues within 4Å: Chain A: V.33, R.34, S.37, E.76 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.37, A:S.37 Water bridges: A:R.34, A:E.76, A:E.76 EDO.18: 6 residues within 4Å: Chain A: T.36, S.37, G.39, D.79, G.80, K.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.37, A:G.80 Water bridges: A:D.79 EDO.19: 4 residues within 4Å: Chain A: R.214, R.222, P.223, D.251 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.214, A:D.251 Water bridges: A:R.214, A:R.219, A:R.222, A:A.224 EDO.20: 1 residues within 4Å: Chain A: R.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.133 Water bridges: A:R.133 EDO.22: 3 residues within 4Å: Chain A: R.30, H.125 Ligands: SO4.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.30, A:R.30 Water bridges: A:E.76, A:E.76 EDO.23: 3 residues within 4Å: Chain A: P.96, L.127, E.170 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.128, A:S.128 EDO.26: 5 residues within 4Å: Chain A: D.24, P.25, E.26, R.104, P.105 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.26, A:R.104, A:R.104 Water bridges: A:E.26 EDO.27: 4 residues within 4Å: Chain A: R.109, P.111, L.270 Ligands: CL.8 No protein-ligand interaction detected (PLIP) EDO.28: 2 residues within 4Å: Chain A: K.200, R.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.200, A:K.200, A:R.204, A:R.204

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.25: 5 residues within 4Å: Chain A: Y.11, F.35, L.41, P.42 Ligands: 01.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DeRatt, L.G. et al., Identification of isoquinolinone DHODH inhibitor isosteres. Bioorg.Med.Chem.Lett. (2024)

Release Date

2024-10-09

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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