SMTL ID : 3mjy.1

Crystal structure of dihydroorotate dehydrogenase from Leishmania major in complex with 5-Aminoorotic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 25 residues within 4Å: Chain A: A.53, A.54, G.55, V.56, K.78, S.79, Y.93, S.100, N.102, M.104, N.162, K.199, I.228, N.229, S.230, G.256, G.257, V.260, C.283, G.284, G.285, V.305, G.306, T.307 Ligands: IJZ.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.56, A:Y.93, A:Y.93 Hydrogen bonds: A:A.54, A:S.79, A:S.79, A:S.79, A:K.199, A:K.199, A:N.229, A:G.257, A:G.285, A:G.306, A:T.307, A:T.307 Water bridges: A:A.54, A:K.78, A:G.284, A:V.286, A:V.286, A:V.286 FMN.7: 25 residues within 4Å: Chain B: A.53, A.54, G.55, V.56, K.78, S.79, Y.93, S.100, N.102, M.104, N.162, K.199, I.228, N.229, S.230, G.256, G.257, V.260, C.283, G.284, G.285, V.305, G.306, T.307 Ligands: IJZ.8 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.56, B:Y.93, B:Y.93 Hydrogen bonds: B:A.54, B:S.79, B:S.79, B:S.79, B:N.162, B:K.199, B:K.199, B:N.229, B:G.257, B:G.285, B:G.306, B:T.307 Water bridges: B:A.54, B:K.78, B:G.284, B:G.284, B:V.286, B:V.286

2 x IJZ: 5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid(Non-covalent)

IJZ.2: 10 residues within 4Å: Chain A: K.78, N.102, S.103, M.104, G.105, L.106, N.162, N.229, S.230 Ligands: FMN.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.102, A:N.102, A:M.104, A:G.105, A:L.106, A:N.162, A:N.229, A:N.229, A:S.230 Water bridges: A:S.134, A:S.134 Salt bridges: A:K.78 IJZ.8: 12 residues within 4Å: Chain B: K.78, N.102, S.103, M.104, G.105, L.106, P.107, N.162, S.164, N.229, S.230 Ligands: FMN.7 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.78, B:K.78, B:N.102, B:N.102, B:M.104, B:G.105, B:L.106, B:N.162, B:N.229, B:N.229, B:S.230 Water bridges: B:G.254 Salt bridges: B:K.78

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: V.236, I.237, Y.259 Chain B: L.261, L.265, L.294 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.237 Water bridges: A:Y.259, A:Y.259, B:D.291 GOL.4: 5 residues within 4Å: Chain A: D.205, F.206, A.207 Chain B: N.233, K.249 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.233, B:K.249, A:F.206, A:A.207 GOL.5: 4 residues within 4Å: Chain A: E.240, T.241, E.242 Chain B: R.344 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.242, B:R.344, B:R.344 Water bridges: B:K.331, B:R.344 GOL.9: 5 residues within 4Å: Chain A: L.261, L.265, L.294 Chain B: V.236, I.237 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.291 Hydrogen bonds: B:I.237 GOL.10: 4 residues within 4Å: Chain A: N.233, K.249 Chain B: D.205, F.206 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.233, B:F.206, B:A.207 Water bridges: A:Q.173

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

SO4.6: 4 residues within 4Å: Chain A: N.43, P.193, H.194, S.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.43, A:S.195, A:S.195 Salt bridges: A:H.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheleski, J. et al., Novel insights for dihydroorotate dehydrogenase class 1A inhibitors discovery. Eur.J.Med.Chem. (2010)

Release Date

2011-02-23

Peptides

Dihydroorotate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase

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