SMTL ID : 6fmd.1

Targeting myeloid differentiation using potent human dihydroorotate dehydrogenase (hDHODH) inhibitors based on 2-hydroxypyrazolo[1,5-a]pyridine scaffold

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

1 x DUH: 2-oxidanyl-~{N}-[2,3,5,6-tetrakis(fluoranyl)-4-phenyl-phenyl]pyrazolo[1,5-a]pyridine-3-carboxamide(Non-covalent)

DUH.1: 19 residues within 4Å: Chain A: Y.37, M.42, L.45, Q.46, P.51, A.54, H.55, A.58, F.61, T.62, L.66, L.67, V.133, R.135, Y.355, L.358, T.359, P.363 Ligands: FMN.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.37, A:A.54, A:H.55, A:A.58, A:F.61, A:L.67, A:V.133, A:Y.355, A:T.359, A:P.363 Hydrogen bonds: A:Q.46, A:R.135, A:R.135, A:T.359 Water bridges: A:T.359, A:T.359 pi-Stacking: A:F.61

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

CL.2: 2 residues within 4Å: Chain A: R.297, S.298 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: R.244 Ligand excluded by PLIP

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.4: 25 residues within 4Å: Chain A: A.94, A.95, G.96, K.99, G.118, S.119, N.144, Y.146, N.180, N.211, K.254, T.282, N.283, T.284, S.304, G.305, L.308, V.332, G.333, G.334, L.354, Y.355, T.356 Ligands: DUH.1, ORO.11 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:N.144, A:Y.146, A:Y.355 Hydrogen bonds: A:A.95, A:K.99, A:S.119, A:S.119, A:N.180, A:N.211, A:K.254, A:K.254, A:N.283, A:S.304, A:G.305, A:G.334, A:Y.355, A:T.356, A:T.356 Water bridges: A:A.95, A:G.333, A:V.335

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

ACT.5: 6 residues within 4Å: Chain A: Q.167, A.168, T.171, L.204, A.205, D.206 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.167 Hydrogen bonds: A:T.171 Water bridges: A:A.168 ACT.6: 5 residues within 4Å: Chain A: R.240, D.241, R.248, L.274, G.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.248 Water bridges: A:R.240 Salt bridges: A:R.240 ACT.7: 1 residues within 4Å: Chain A: R.245 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.245 ACT.8: 2 residues within 4Å: Chain A: K.306, P.307 No protein-ligand interaction detected (PLIP) ACT.9: 2 residues within 4Å: Chain A: H.40, T.44 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.40 ACT.10: 1 residues within 4Å: Chain A: R.145 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.145 Salt bridges: A:R.145

1 x ORO: OROTIC ACID(Non-covalent)

ORO.11: 10 residues within 4Å: Chain A: K.99, N.144, R.145, Y.146, G.147, F.148, N.211, N.283, T.284 Ligands: FMN.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.148 Hydrogen bonds: A:N.144, A:N.144, A:N.144, A:G.147, A:F.148, A:N.211, A:N.283, A:N.283 Salt bridges: A:K.99

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 4 residues within 4Å: Chain A: G.275, I.276, D.277, R.326 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.275, A:G.275, A:D.277, A:D.277 GOL.13: 3 residues within 4Å: Chain A: A.70, Y.108, K.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.109 GOL.14: 4 residues within 4Å: Chain A: E.126, G.127, N.128, R.130 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.126, A:N.128 Water bridges: A:E.126, A:R.130, A:R.132 GOL.15: 3 residues within 4Å: Chain A: P.122, K.123, E.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.196

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

PGE.16: 8 residues within 4Å: Chain A: H.100, P.124, Q.125, E.126, N.149, S.150, H.151 Ligands: PGE.17 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.149 Water bridges: A:H.100, A:E.126, A:R.132, A:H.151 PGE.17: 5 residues within 4Å: Chain A: P.124, H.151, V.155, R.159 Ligands: PGE.16 No protein-ligand interaction detected (PLIP) PGE.18: 5 residues within 4Å: Chain A: D.50, E.52, S.53, R.56, R.130 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.52, A:E.52 PGE.19: 5 residues within 4Å: Chain A: R.81, G.325, R.326, P.328, S.350 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.81, A:S.350 PGE.20: 7 residues within 4Å: Chain A: L.83, G.84, R.240, R.245, R.248, P.249, D.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.248 Water bridges: A:A.250 PGE.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sainas, S. et al., Targeting Myeloid Differentiation Using Potent 2-Hydroxypyrazolo[1,5- a]pyridine Scaffold-Based Human Dihydroorotate Dehydrogenase Inhibitors. J. Med. Chem. (2018)

Release Date

2018-07-11

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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