SMTL ID : 6jme.1

Crystal structure of human DHODH in complex with inhibitor 0946

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 30 residues within 4Å: Chain A: A.65, A.66, G.67, K.70, G.89, S.90, V.104, V.113, N.115, Y.117, F.119, N.151, N.182, K.225, T.253, N.254, T.255, S.275, G.276, L.279, V.303, G.304, G.305, V.306, L.325, Y.326, T.327, A.328 Ligands: ORO.2, BVU.9 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:N.115, A:Y.117, A:Y.326 Hydrogen bonds: A:K.70, A:S.90, A:S.90, A:N.151, A:K.225, A:T.253, A:N.254, A:G.276, A:G.305, A:Y.326, A:T.327, A:T.327 Water bridges: A:A.66, A:G.304, A:G.304, A:Q.324

1 x ORO: OROTIC ACID(Non-covalent)

ORO.2: 14 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, G.273 Ligands: FMN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.119 Hydrogen bonds: A:N.115, A:N.115, A:N.115, A:Y.117, A:G.118, A:F.119, A:N.182, A:N.187, A:N.254, A:N.254, A:T.255 Water bridges: A:S.185, A:S.185 Salt bridges: A:K.70

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

SO4.3: 3 residues within 4Å: Chain A: R.215, V.217, H.218 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.215, A:H.218 SO4.4: 3 residues within 4Å: Chain A: A.189, G.190, R.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.190 Water bridges: A:L.191, A:R.192 Salt bridges: A:R.192 SO4.10: 4 residues within 4Å: Chain A: T.231, Q.233, D.234 Ligands: NA.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.231

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

ACT.5: 8 residues within 4Å: Chain A: Q.138, A.139, T.142, L.148, L.175, A.176, D.177 Ligands: NA.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.138 ACT.6: 2 residues within 4Å: Chain A: V.126, R.130 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.130 Salt bridges: A:R.130 ACT.7: 4 residues within 4Å: Chain A: R.27, H.71, N.120, H.122 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.120 Water bridges: A:S.121 Salt bridges: A:R.27, A:H.71, A:H.122

1 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.8: 10 residues within 4Å: Chain A: E.109, D.110, Q.111, P.260, A.261, K.277, P.278, L.279, R.280, D.281 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.260, A:K.277, A:P.278

1 x BVU: 3-[3,5-bis(fluoranyl)-4-(2-fluorophenyl)phenyl]benzo[f]benzotriazole-4,9-dione(Non-covalent)

BVU.9: 27 residues within 4Å: Chain A: Y.8, L.12, M.13, L.16, Q.17, P.22, A.25, H.26, L.28, A.29, F.32, T.33, L.37, L.38, P.39, F.68, M.81, V.104, R.106, V.113, Y.117, Y.326, L.329, T.330, G.333, P.334 Ligands: FMN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.16, A:P.22, A:H.26, A:F.32, A:L.38, A:V.104, A:Y.326, A:P.334 Hydrogen bonds: A:R.106, A:R.106

3 x NA: SODIUM ION(Non-functional Binders)

NA.11: 4 residues within 4Å: Chain A: Q.135, Q.138, A.139 Ligands: ACT.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.135 NA.12: 4 residues within 4Å: Chain A: T.231, S.232, Q.233 Ligands: SO4.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.231, A:S.232, A:Q.233 NA.13: 5 residues within 4Å: Chain A: A.176, D.177, V.217, R.219, P.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.217, A:R.219 Water bridges: A:H.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zuo, Z. et al., Bifunctional Naphtho[2,3- d ][1,2,3]triazole-4,9-dione Compounds Exhibit Antitumor Effects In Vitro and In Vivo by Inhibiting Dihydroorotate Dehydrogenase and Inducing Reactive Oxygen Species Production. J.Med.Chem. (2020)

Release Date

2020-03-18

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