SMTL ID : 9bko.1

DHODH in complex with Ligand 26

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 25 residues within 4Å: Chain A: A.66, A.67, G.68, K.71, G.90, S.91, N.116, Y.118, N.152, N.183, K.226, T.254, N.255, T.256, S.276, G.277, L.280, V.304, G.305, G.306, L.326, Y.327, T.328 Ligands: ORO.2, 01.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:N.116, A:Y.118, A:Y.327 Hydrogen bonds: A:A.67, A:K.71, A:S.91, A:S.91, A:N.152, A:K.226, A:K.226, A:N.255, A:G.277, A:G.306, A:Y.327, A:T.328, A:T.328 Water bridges: A:A.67, A:G.305, A:G.305

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 13 residues within 4Å: Chain A: K.71, N.116, R.117, Y.118, G.119, F.120, N.183, S.186, P.187, N.188, N.255, T.256 Ligands: FMN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.120 Hydrogen bonds: A:N.116, A:N.116, A:N.116, A:G.119, A:F.120, A:N.183, A:N.188, A:N.255, A:N.255 Water bridges: A:S.186, A:S.186 Salt bridges: A:K.71

1 x 01: (2P,6P)-6-[4-ethyl-3-(hydroxymethyl)-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl]-7-fluoro-2-(2-methylphenyl)-4-[(2R)-1,1,1-trifluoropropan-2-yl]isoquinolin-1(2H)-one

01.3: 22 residues within 4Å: Chain A: Y.9, M.14, L.17, Q.18, L.21, P.23, A.26, H.27, L.29, A.30, F.33, T.34, L.38, L.39, F.69, R.107, V.114, Y.327, L.330, T.331, P.335 Ligands: FMN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.9, A:L.17, A:A.30, A:F.33, A:L.39, A:L.330, A:T.331, A:P.335 Hydrogen bonds: A:Q.18 Water bridges: A:T.331

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

SO4.4: 3 residues within 4Å: Chain A: A.190, G.191, R.193 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.191 Water bridges: A:T.189, A:L.192, A:R.193 Salt bridges: A:R.193 SO4.5: 3 residues within 4Å: Chain A: R.216, V.218, H.219 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.216, A:H.219 SO4.6: 2 residues within 4Å: Chain A: R.217, R.220 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.217, A:R.217 Salt bridges: A:R.220

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

CL.7: 3 residues within 4Å: Chain A: Q.136, P.175, H.219 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: T.272, G.273 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: P.23, F.106, R.107, L.268 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: P.94, K.95, L.125, S.126, E.168 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.126, A:E.168 Water bridges: A:S.126, A:S.126 GOL.11: 2 residues within 4Å: Chain A: K.198, R.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.198, A:R.202

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

ACT.12: 2 residues within 4Å: Chain A: S.126, H.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.126 Salt bridges: A:H.130 ACT.13: 6 residues within 4Å: Chain A: Q.139, A.140, T.143, L.176, A.177, D.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.143 Water bridges: A:E.144 ACT.14: 6 residues within 4Å: Chain A: E.24, H.27, K.71, H.72, Y.118, N.121 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.121 Water bridges: A:H.27, A:R.28 Salt bridges: A:H.27, A:H.72 ACT.15: 4 residues within 4Å: Chain A: D.282, T.285, Q.286, R.289 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.282, A:Q.286 Salt bridges: A:R.289 ACT.16: 3 residues within 4Å: Chain A: T.232, Q.234, D.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.235 Water bridges: A:Q.234 ACT.17: 5 residues within 4Å: Chain A: H.57, A.177, R.217, V.218, R.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.177, A:R.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DeRatt, L.G. et al., Discovery of JNJ-74856665: A Novel Isoquinolinone DHODH Inhibitor for the Treatment of AML. J.Med.Chem. (2024)

Release Date

2024-07-03

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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