SMTL ID : 9dhg.1

DHODH in complex with Compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 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:S.278, A:G.279, A:G.308, A:Y.329, 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 15 PLIP interactions: 15 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, A:T.258 Water bridges: A:S.188, A:S.188 Salt bridges: A:K.73

1 x 01: (3P,7P)-7-[4-ethyl-3-(hydroxymethyl)-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl]-6-fluoro-3-(2-methylphenyl)-1-(propan-2-yl)quinolin-4(1H)-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.26 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.11, A:L.19, A:L.23, A:A.32, A:F.35, A:L.41, A:V.107, A:L.332, A:T.333, A:P.337 Hydrogen bonds: A:Q.20, A:Y.329 pi-Stacking: A:F.35

5 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 SO4.13: 3 residues within 4Å: Chain A: S.128, E.131, H.132 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.128, A:S.128 Water bridges: A:S.128, A:E.131 Salt bridges: A:H.132 SO4.18: 3 residues within 4Å: Chain A: A.192, G.193, R.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.193 Water bridges: A:L.194, A:R.195 Salt bridges: A:R.195 SO4.19: 4 residues within 4Å: Chain A: D.284, T.287, Q.288, R.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.284, A:Q.288 Salt bridges: A:R.291

2 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.180 Water bridges: A:E.146 ACT.25: 3 residues within 4Å: Chain A: T.234, Q.236, D.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.234, A:D.237

10 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: 6 residues within 4Å: Chain A: P.25, F.108, R.109, L.270 Ligands: EDO.20, EDO.21 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: Y.82, K.83 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: T.234, S.235 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: T.274, G.275 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain A: P.98, H.125, G.126, L.127, S.128, V.129 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: R.214, D.215 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: Q.313, L.316, Q.354 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: A.179, V.220, R.222 Ligand excluded by PLIP

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

EDO.20: 3 residues within 4Å: Chain A: R.109, P.111 Ligands: CL.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.109 EDO.21: 5 residues within 4Å: Chain A: P.25, P.105, V.107, F.108 Ligands: CL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.107 EDO.22: 5 residues within 4Å: Chain A: P.98, Q.99, E.100, S.124, H.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.99, A:S.124 EDO.24: 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.27: 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 EDO.28: 1 residues within 4Å: Chain A: P.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.128 Water bridges: A:L.127, A:S.128

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.23: 7 residues within 4Å: Chain A: E.26, H.29, R.30, K.73, H.74, Y.120, N.123 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.26, A:E.26, A:R.30, A:H.74, A:Y.120, A:N.123 Water bridges: A:H.74, A:E.76, A:H.125 GOL.29: 3 residues within 4Å: Chain A: A.4, T.5, G.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.4, A:G.6

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

PGE.26: 4 residues within 4Å: Chain A: F.35, L.40, L.41 Ligands: 01.3 No protein-ligand interaction detected (PLIP)

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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