SMTL ID : 6j3b.1

Crystal structure of human DHODH in complex with inhibitor 1289

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.215, V.217, H.218 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.215 Salt bridges: A:R.215, A:H.218 SO4.2: 4 residues within 4Å: Chain A: A.189, G.190, L.191, 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 SO4.15: 2 residues within 4Å: Chain A: R.216, R.219 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.216, A:R.216, A:R.219 Salt bridges: A:R.219 SO4.16: 9 residues within 4Å: Chain A: H.56, A.176, D.177, R.216, V.217, H.218, R.219, P.220 Ligands: ACT.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.177, A:V.217 Water bridges: A:H.56, A:A.221 Salt bridges: A:H.56 SO4.17: 6 residues within 4Å: Chain A: R.27, H.71, R.101, R.103, N.120, H.122 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.101, A:N.120 Water bridges: A:E.23, A:H.71, A:R.103, A:R.103, A:R.103, A:S.121 Salt bridges: A:R.27, A:H.71, A:H.122 SO4.18: 3 residues within 4Å: Chain A: S.232, K.235, E.289 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.232 Water bridges: A:S.232, A:K.235, A:K.235, A:E.289 Salt bridges: A:K.235

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 31 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.4, B5O.5, NA.23 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:K.225, A:T.253, A:N.254, A:S.275, A:G.276, A:G.305, A:Y.326, A:T.327, A:T.327 Water bridges: A:A.66, A:V.306, A:V.306, A:Q.324

1 x ORO: OROTIC ACID(Non-covalent)

ORO.4: 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.3 14 PLIP interactions: 14 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, A:S.185 Salt bridges: A:K.70

1 x B5O: (6R)-1-[3,5-bis(fluoranyl)-4-[2-fluoranyl-5-(hydroxymethyl)phenyl]phenyl]-6-propan-2-yl-6,7-dihydro-5H-benzotriazol-4-one(Non-covalent)

B5O.5: 26 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, F.68, M.81, V.104, R.106, V.113, Y.117, Y.326, L.329, T.330, G.333, P.334 Ligands: FMN.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.16, A:H.26, A:A.29, A:Y.326, A:T.330, A:P.334 Hydrogen bonds: A:Y.8, A:R.106, A:R.106

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

LDA.6: 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.111, A:K.277, A:K.277, A:K.277 Water bridges: A:D.281

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 4 residues within 4Å: Chain A: T.231, Q.233, D.234 Ligands: DMS.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.231 Water bridges: A:Q.233 DMS.8: 4 residues within 4Å: Chain A: T.231, S.232, Q.233 Ligands: DMS.7 No protein-ligand interaction detected (PLIP)

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

ACT.9: 8 residues within 4Å: Chain A: Q.138, A.139, T.142, L.148, L.175, A.176, D.177 Ligands: SO4.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.177 Water bridges: A:E.143 ACT.10: 6 residues within 4Å: Chain A: E.97, G.98, N.99, P.100, R.101, R.103 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.97 Hydrogen bonds: A:E.97, A:R.101 Water bridges: A:R.103 Salt bridges: A:R.101, A:R.103 ACT.11: 6 residues within 4Å: Chain A: P.93, K.94, L.124, S.125, E.167, V.171 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.124 Water bridges: A:S.125 Salt bridges: A:K.94 ACT.12: 2 residues within 4Å: Chain A: V.126, R.130 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.73 Salt bridges: A:R.130 ACT.13: 2 residues within 4Å: Chain A: K.197, R.201 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.197 Salt bridges: A:K.197, A:R.201 ACT.14: 5 residues within 4Å: Chain A: A.41, R.42, F.43, P.335, G.338 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.41, A:F.43 Hydrogen bonds: A:R.42, A:F.43 Water bridges: A:D.4, A:D.4

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

CL.19: 2 residues within 4Å: Chain A: R.268, S.269 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain A: R.132, Q.135, L.175 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain A: R.215 Ligand excluded by PLIP

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

NA.22: 4 residues within 4Å: Chain A: G.196, K.197, D.234, D.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.197, A:D.234, A:D.237 NA.23: 7 residues within 4Å: Chain A: V.303, G.304, G.305, V.306, Q.324, L.325 Ligands: FMN.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.304, A:G.304, A:V.306 Water bridges: A:T.327

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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