SMTL ID : 6j3c.1

Crystal structure of human DHODH in complex with inhibitor 1291

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

SO4.1: 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 SO4.2: 5 residues within 4Å: Chain A: R.132, Q.135, P.174, L.175, H.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.132, A:Q.135 Water bridges: A:R.132 Salt bridges: A:H.218 SO4.3: 8 residues within 4Å: Chain A: H.56, A.176, D.177, R.216, V.217, H.218, R.219, P.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.219, A:R.219 Salt bridges: A:H.56 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

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 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.6, B5X.7 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:N.115, A:Y.117, A:Y.326, 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:V.306, A:Q.324

1 x ORO: OROTIC ACID(Non-covalent)

ORO.6: 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.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.119 Hydrogen bonds: 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 Salt bridges: A:K.70

1 x B5X: (6R)-1-[4-[3-(dimethylamino)phenyl]-3,5-bis(fluoranyl)phenyl]-6-propan-2-yl-6,7-dihydro-5H-benzotriazol-4-one(Non-covalent)

B5X.7: 28 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, T.327, L.329, T.330, G.333, P.334 Ligands: FMN.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.26, A:F.32, A:L.38, A:V.104, A:Y.326, A:T.330, A:P.334 Hydrogen bonds: A:R.106, A:R.106

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

LDA.8: 11 residues within 4Å: Chain A: P.108, E.109, D.110, Q.111, P.260, A.261, K.277, P.278, R.280, D.281, L.282 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.111, A:Q.111, A:K.277, A:K.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, T. et al., A novel series of human dihydroorotate dehydrogenase inhibitors discovered by in vitro screening: inhibition activity and crystallographic binding mode. Febs Open Bio (2019)

Release Date

2019-08-21

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial

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