SMTL ID : 7z6c.1

Crystal structure of human Dihydroorotate Dehydrogenase in complex with the inhibitor 2-Hydroxy-N-(2-ispropyl-5-methyl-4-phenoxyphenyl)pyrazolo[1,5-a]pyridine-3-carboxamide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 26 residues within 4Å: Chain A: A.65, A.66, G.67, K.70, G.89, S.90, V.113, N.115, Y.117, N.151, N.182, K.225, T.253, N.254, T.255, S.275, G.276, L.279, V.303, G.304, G.305, L.325, Y.326, T.327 Ligands: ORO.2, IEQ.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:N.115, A:Y.117, A:Y.326 Hydrogen bonds: A:A.66, A:K.70, A:S.90, A:S.90, A:N.151, A:N.182, A:K.225, A:T.253, A:N.254, A:S.275, A:S.275, A:G.276, A:G.305, A:Y.326, A:T.327, A:T.327 Water bridges: A:A.66, A:G.304, A:V.306, A:V.306, A:V.306

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 13 residues within 4Å: Chain A: K.70, N.115, R.116, Y.117, G.118, F.119, N.182, S.185, P.186, N.187, N.254, T.255 Ligands: FMN.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.115, A:N.115, A:G.118, A:F.119, A:N.182, A:N.187, A:N.254, A:N.254 Salt bridges: A:K.70

1 x IEQ: ~{N}-(5-methyl-4-phenoxy-2-propan-2-yl-phenyl)-2-oxidanyl-pyrazolo[1,5-a]pyridine-3-carboxamide(Non-covalent)

IEQ.3: 24 residues within 4Å: Chain A: Y.8, L.12, M.13, L.16, Q.17, L.20, P.22, A.25, H.26, L.28, A.29, L.37, L.38, F.68, M.81, V.104, R.106, V.113, Y.326, L.329, T.330, G.333, P.334 Ligands: FMN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.8, A:L.12, A:L.16, A:A.25, A:H.26, A:A.29, A:A.29, A:V.104, A:Y.326, A:L.329, A:P.334 Hydrogen bonds: A:Q.17, A:R.106, A:T.330 Water bridges: A:T.330

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.4: 8 residues within 4Å: Chain A: D.281, T.284, Q.285, R.288, E.314, R.317, D.363, R.366 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.281, A:Q.285, A:R.288, A:R.317, A:R.366 Water bridges: A:R.288

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

ACT.5: 3 residues within 4Å: Chain A: R.215, V.217, H.218 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.217 Salt bridges: A:R.215, A:H.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sainas, S. et al., Targeting Acute Myelogenous Leukemia Using Potent Human Dihydroorotate Dehydrogenase Inhibitors Based on the 2-Hydroxypyrazolo[1,5- a ]pyridine Scaffold: SAR of the Aryloxyaryl Moiety. J.Med.Chem. (2022)

Release Date

2022-10-12

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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