SMTL ID : 6lp8.1

Crystal structure of human DHODH in complex with inhibitor 1243

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 30 residues within 4Å: Chain A: H.26, 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 Ligands: ORO.2, B6O.9 22 PLIP interactions: 22 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:N.182, 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:V.306, A:V.306, 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 13 PLIP interactions: 13 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 Salt bridges: A:K.70

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

SO4.3: 3 residues within 4Å: Chain A: R.215, V.217, H.218 4 PLIP interactions: 4 interactions with chain A Water bridges: A:V.217, A:V.217 Salt bridges: A:R.215, A:H.218 SO4.4: 3 residues within 4Å: Chain A: A.189, G.190, R.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.190 Salt bridges: A:R.192

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

ACT.5: 9 residues within 4Å: Chain A: H.56, Q.138, A.139, T.142, L.175, A.176, D.177 Ligands: NA.12, NA.14 No protein-ligand interaction detected (PLIP) ACT.6: 2 residues within 4Å: Chain A: V.126, R.130 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.130, A:R.130 Salt bridges: A:R.130 ACT.8: 4 residues within 4Å: Chain A: T.231, S.232 Ligands: ACT.11, NA.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.232 ACT.10: 7 residues within 4Å: Chain A: D.21, P.22, P.102, V.104, F.105, R.106, L.267 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.102 ACT.11: 5 residues within 4Å: Chain A: T.231, Q.233, D.234 Ligands: ACT.8, NA.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.231, A:Q.233 Hydrogen bonds: A:T.231

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

LDA.7: 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 B6O: 3-[4-[3-(dimethylamino)phenyl]-3,5-bis(fluoranyl)phenyl]benzo[f]benzotriazole-4,9-dione(Non-covalent)

B6O.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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.26, A:F.32, A:V.104, A:Y.326, A:T.330, A:P.334 Hydrogen bonds: A:R.106 pi-Stacking: A:F.32

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

NA.12: 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.13: 5 residues within 4Å: Chain A: T.231, S.232, Q.233 Ligands: ACT.8, ACT.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.232, A:Q.233 NA.14: 5 residues within 4Å: Chain A: D.177, V.217, R.219, P.220 Ligands: ACT.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.176, 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

2020-09-30

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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