SMTL ID : 6vnd.1

Quaternary Complex of human dihydroorotate dehydrogenase (DHODH) with flavin mononucleotide (FMN), orotic acid and AG-636

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

1 x R4P: 1-methyl-5-(2'-methyl[1,1'-biphenyl]-4-yl)-1H-benzotriazole-7-carboxylic acid(Non-covalent)

R4P.1: 17 residues within 4Å: Chain A: Y.10, L.14, M.15, L.18, Q.19, P.24, A.27, H.28, A.31, T.35, L.39, L.40, R.108, Y.328, T.332, P.336 Ligands: DDQ.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.10, A:L.14, A:A.27, A:A.31, A:L.40, A:P.336 Hydrogen bonds: A:Q.19 Salt bridges: A:R.108

2 x DET: UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE(Non-covalent)

DET.2: 11 residues within 4Å: Chain A: H.28, R.29, K.72, H.73, P.97, Q.98, E.99, N.122, S.123, H.124 Ligands: NA.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.97, A:E.99, A:N.122 Hydrogen bonds: A:R.29, A:Y.119 DET.3: 6 residues within 4Å: Chain A: E.111, D.112, Q.113, P.262, K.279, P.280 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.113 Water bridges: A:A.263

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

DDQ.4: 8 residues within 4Å: Chain A: Y.10, L.14, L.18, F.34, L.39, L.40, P.41 Ligands: R4P.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.14, A:L.18, A:F.34, A:F.34 Hydrogen bonds: A:L.40 DDQ.5: 4 residues within 4Å: Chain A: R.319, Q.353, F.355, A.364 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.353, A:F.355

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

CL.6: 3 residues within 4Å: Chain A: Q.137, P.176, H.220 Ligand excluded by PLIP

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

NA.7: 5 residues within 4Å: Chain A: E.25, R.29, R.103, R.105 Ligands: DET.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.29, A:R.29, A:R.105 NA.8: 2 residues within 4Å: Chain A: S.234, E.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.234, A:E.238 NA.9: 5 residues within 4Å: Chain A: K.199, R.203, S.242, V.243, E.246 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.199, A:R.203, A:R.203, A:E.246

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.10: 24 residues within 4Å: Chain A: A.67, A.68, G.69, K.72, G.91, S.92, N.117, Y.119, N.153, N.184, K.227, T.255, N.256, T.257, S.277, G.278, L.281, V.305, G.306, G.307, L.327, Y.328, T.329 Ligands: ORO.11 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:N.117, A:Y.119, A:Y.328, A:Y.328 Hydrogen bonds: A:A.68, A:K.72, A:S.92, A:S.92, A:N.153, A:N.184, A:K.227, A:K.227, A:N.256, A:S.277, A:S.277, A:G.278, A:G.307, A:Y.328, A:T.329, A:T.329 Water bridges: A:A.68, A:G.306, A:G.306

1 x ORO: OROTIC ACID(Non-covalent)

ORO.11: 13 residues within 4Å: Chain A: K.72, N.117, R.118, Y.119, G.120, F.121, N.184, S.187, P.188, N.189, N.256, T.257 Ligands: FMN.10 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.121 Hydrogen bonds: A:N.117, A:N.117, A:N.117, A:G.120, A:F.121, A:N.184, A:N.189, A:N.256, A:N.256 Water bridges: A:S.187, A:S.187 Salt bridges: A:K.72

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

ACT.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.13: 4 residues within 4Å: Chain A: K.199, E.238, D.239, S.242 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.199 ACT.14: 2 residues within 4Å: Chain A: R.213, R.221 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.221 Salt bridges: A:R.213

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 3 residues within 4Å: Chain A: D.78, Y.81, L.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.78 GOL.16: 4 residues within 4Å: Chain A: P.102, R.103, P.104, R.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.102, A:R.103, A:R.118 GOL.17: 7 residues within 4Å: Chain A: Q.137, Q.140, A.141, T.144, L.177, A.178, D.179 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.137, A:A.141, A:T.144, A:T.144, A:D.179 GOL.18: 2 residues within 4Å: Chain A: R.29, L.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.29 GOL.19: 4 residues within 4Å: Chain A: Y.293, A.294, Q.297, H.366 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.363, A:H.366 GOL.20: 2 residues within 4Å: Chain A: G.20, L.21 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McDonald, G. et al., Selective Vulnerability to Pyrimidine Starvation in Hematologic Malignancies Revealed by AG-636, a Novel Clinical-Stage Inhibitor of Dihydroorotate Dehydrogenase. Mol.Cancer Ther. (2020)

Release Date

2020-11-04

Peptides

Dihydroorotate dehydrogenase (quinone), mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroorotate dehydrogenase (quinone), mitochondrial