SMTL ID : 8rak.1

Crystal structure of human Dihydroorotate Dehydrogenase in complex with the inhibitor 2-Hydroxy-N-(2-isopropyl-5-methyl-4-(pyridin-4-yloxy)phenyl)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.89, A.90, G.91, K.94, G.113, S.114, V.137, N.139, Y.141, N.175, N.206, K.249, T.277, N.278, T.279, S.299, G.300, L.303, V.327, G.328, G.329, L.349, Y.350, T.351 Ligands: ORO.2, YMH.3 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:N.139, A:Y.141, A:Y.350 Hydrogen bonds: A:K.94, A:S.114, A:S.114, A:N.175, A:K.249, A:K.249, A:T.277, A:N.278, A:S.299, A:S.299, A:G.300, A:G.329, A:Y.350, A:T.351, A:T.351 Water bridges: A:A.90, A:G.328, A:V.330, A:V.330, A:V.330

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 13 residues within 4Å: Chain A: K.94, N.139, R.140, Y.141, G.142, F.143, N.206, S.209, P.210, N.211, N.278, T.279 Ligands: FMN.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.139, A:G.142, A:F.143, A:N.206, A:N.278, A:N.278 Water bridges: A:S.209, A:S.209 Salt bridges: A:K.94

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

YMH.3: 23 residues within 4Å: Chain A: Y.32, M.37, L.40, Q.41, L.44, P.46, A.49, H.50, A.53, F.56, T.57, L.62, F.92, M.105, V.128, R.130, V.137, Y.350, L.353, T.354, G.357, P.358 Ligands: FMN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.40, A:Q.41, A:A.49, A:H.50, A:A.53, A:V.128, A:Y.350, A:L.353, A:P.358 Hydrogen bonds: A:Q.41, A:R.130

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

ACT.4: 3 residues within 4Å: Chain A: T.255, Q.257, D.258 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.255, A:Q.257 ACT.5: 4 residues within 4Å: Chain A: R.51, H.95, H.146 Ligands: ACT.6 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.97 Salt bridges: A:R.51, A:H.95, A:H.146 ACT.6: 7 residues within 4Å: Chain A: H.50, R.51, K.94, H.95, Y.141, N.144 Ligands: ACT.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.51 Hydrogen bonds: A:N.144 Water bridges: A:H.50 Salt bridges: A:H.50, A:H.95 ACT.7: 4 residues within 4Å: Chain A: D.305, T.308, Q.309, R.312 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.305 Water bridges: A:D.305, A:R.312 Salt bridges: A:R.312 ACT.8: 1 residues within 4Å: Chain A: R.154 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.154 Salt bridges: A:R.154

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

SO4.9: 2 residues within 4Å: Chain A: R.240, R.243 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.240 Salt bridges: A:R.243 SO4.10: 3 residues within 4Å: Chain A: R.239, V.241, H.242 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.239 Salt bridges: A:R.239, A:H.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alberti, M. et al., An alternative conformation of the N-terminal loop of human dihydroorotate dehydrogenase drives binding to a potent antiproliferative agent. Acta Crystallogr D Struct Biol (2024)

Release Date

2024-06-19

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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