SMTL ID : 8dhf.1

DHODH IN COMPLEX WITH LIGAND 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 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, T6L.3 22 PLIP interactions: 22 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:N.185, A:K.228, A:K.228, A:N.257, A:S.278, A:G.279, A:G.308, A:Y.329, A:T.330, A:T.330 Water bridges: A:A.69, A:G.307, A:G.307

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 10 residues within 4Å: Chain A: K.73, N.118, R.119, Y.120, G.121, F.122, N.185, N.257, T.258 Ligands: FMN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.122 Hydrogen bonds: A:N.118, A:N.118, A:N.118, A:G.121, A:F.122, A:N.185, A:N.257, A:N.257 Salt bridges: A:K.73

1 x T6L: (6M)-N-(2-chloro-6-fluorophenyl)-6-[4-ethyl-3-(hydroxymethyl)-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl]-5-fluoro-2-{[(2S)-1,1,1-trifluoropropan-2-yl]oxy}pyridine-3-carboxamide(Non-covalent)

T6L.3: 22 residues within 4Å: Chain A: Y.11, M.16, L.19, Q.20, L.23, P.25, A.28, H.29, L.31, A.32, F.35, T.36, L.40, L.41, F.71, R.109, V.116, Y.329, L.332, T.333, P.337 Ligands: FMN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.11, A:L.19, A:A.28, A:A.32, A:F.35, A:L.41, A:T.333, A:P.337 Hydrogen bonds: A:Q.20 Water bridges: A:T.333 Halogen bonds: A:A.32, A:T.36

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

ACT.4: 2 residues within 4Å: Chain A: K.280, P.281 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.280 ACT.13: 6 residues within 4Å: Chain A: Q.141, A.142, T.145, A.179, D.180 Ligands: SO4.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.145 Water bridges: A:A.142 ACT.15: 3 residues within 4Å: Chain A: H.125, V.129, R.133 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.125, A:R.133 ACT.16: 4 residues within 4Å: Chain A: Q.99, N.158, K.159, T.160 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.99 Hydrogen bonds: A:Q.99, A:N.158, A:K.159, A:T.160

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: E.26, H.29, R.30, K.73, H.74, Y.120, N.123 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.26, A:R.30, A:N.123 Water bridges: A:H.29, A:H.74 GOL.6: 6 residues within 4Å: Chain A: R.55, V.56, S.324, T.360, I.363 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.324 GOL.7: 6 residues within 4Å: Chain A: Y.294, G.299, T.360, I.363, R.368 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.294, A:G.299, A:R.368, A:R.368 GOL.9: 3 residues within 4Å: Chain A: Q.212, D.215, G.216 No protein-ligand interaction detected (PLIP) GOL.12: 5 residues within 4Å: Chain A: G.58, H.59, K.60, T.145, E.146 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.58, A:K.60, A:K.60, A:E.146 GOL.18: 6 residues within 4Å: Chain A: P.96, K.97, L.127, S.128, E.170, V.174 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.128, A:E.170 GOL.19: 4 residues within 4Å: Chain A: K.200, E.239, D.240, S.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.200, A:E.239 GOL.20: 4 residues within 4Å: Chain A: R.262, P.263, R.271, S.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.263, A:S.272 Water bridges: A:G.265

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

SO4.8: 4 residues within 4Å: Chain A: R.214, D.215, R.222 Ligands: SO4.17 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.214, A:R.222 SO4.10: 3 residues within 4Å: Chain A: R.218, R.219, R.222 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.219 Water bridges: A:R.218, A:R.218, A:V.220, A:R.222, A:R.222 Salt bridges: A:R.218 SO4.11: 2 residues within 4Å: Chain A: R.218, H.221 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.218, A:H.221 SO4.14: 8 residues within 4Å: Chain A: H.59, A.179, D.180, V.220, H.221, R.222, P.223 Ligands: ACT.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.222 Salt bridges: A:H.59 SO4.17: 6 residues within 4Å: Chain A: L.211, R.214, D.215, L.248, G.249 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.215 Water bridges: A:R.214 Salt bridges: A:R.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cisar, J.S. et al., N -Heterocyclic 3-Pyridyl Carboxamide Inhibitors of DHODH for the Treatment of Acute Myelogenous Leukemia. J.Med.Chem. (2022)

Release Date

2022-08-17

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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