SMTL ID : 6et4.1

HUMAN DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH NOVEL INHIBITOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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: DOR.2, SDV.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:N.116, A:Y.118, A:Y.327, 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:S.276, A:G.277, A:G.306, A:Y.327, A:T.328 Water bridges: A:A.67, A:G.305, A:V.307

1 x DOR: (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID(Non-covalent)

DOR.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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.120 Hydrogen bonds: A:N.116, A:N.116, A:Y.118, A:G.119, A:F.120, A:N.183, A:N.188, A:N.255, A:N.255, A:T.256 Water bridges: A:S.186, A:S.186 Salt bridges: A:K.71

1 x SDV: N-[(4R)-1-(2-fluorophenyl)-4,5,6,7-tetrahydroindazol-4-yl]-2,1-benzoxazole-3-carboxamide(Non-covalent)

SDV.3: 18 residues within 4Å: Chain A: Y.9, M.14, P.23, A.26, H.27, A.30, F.33, T.34, L.38, L.39, F.69, V.105, Y.327, L.330, T.331, P.335 Ligands: FMN.1, DDQ.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.23, A:A.26, A:H.27, A:A.30, A:F.33, A:L.39, A:V.105, A:T.331, A:P.335 Hydrogen bonds: A:A.26, A:Y.327 Water bridges: A:R.107, A:T.331

1 x DDQ: DECYLAMINE-N,N-DIMETHYL-N-OXIDE(Non-covalent)

DDQ.4: 6 residues within 4Å: Chain A: Y.9, L.13, F.33, L.38, L.39 Ligands: SDV.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.13, A:F.33

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 6 residues within 4Å: Chain A: Q.139, A.140, T.143, L.176, A.177, D.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.178 ACY.6: 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 ACY.7: 2 residues within 4Å: Chain A: R.28, H.123 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.28, A:N.121 Salt bridges: A:R.28, A:H.72, A:H.123 ACY.8: 7 residues within 4Å: Chain A: E.24, H.27, R.28, K.71, H.72, Y.118, N.121 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.118 Hydrogen bonds: A:N.121 Salt bridges: A:H.27, A:R.28, A:H.72

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: P.94, K.95, V.172 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.126, A:E.168, A:E.168 GOL.10: 1 residues within 4Å: Chain A: R.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.131, A:R.131 GOL.11: 3 residues within 4Å: Chain A: K.198, A.199, R.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.198, A:K.198, A:A.199, A:R.202, A:R.202

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

SO4.12: 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 SO4.13: 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.220 Salt bridges: A:R.220

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

CL.14: 2 residues within 4Å: Chain A: R.269, S.270 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: D.5, P.40, R.41 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: T.232, S.233 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ladds, M.J.G.W. et al., A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage. Nat Commun (2018)

Release Date

2018-03-28

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

Related Entries With Identical Sequence