SMTL ID : 5e93.1

Crystal Structure of Trypanosoma cruzi Dihydroorotate Dehydrogenase in Complex with Neq0071

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-dimer

Ligands

2 x 5LL: 5-[(E)-3-(furan-2-yl)prop-2-enylidene]-1,3-diazinane-2,4,6-trione(Non-covalent)

5LL.1: 16 residues within 4Å: Chain A: S.46, C.47, T.48, N.69, M.71, G.72, L.73, N.75, S.101, N.129, C.132, P.133, N.134, N.196, S.197 Ligands: FMN.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.48 Hydrogen bonds: A:N.69, A:N.69, A:M.71, A:G.72, A:N.129, A:N.134, A:N.196, A:N.196, A:S.197 5LL.23: 17 residues within 4Å: Chain B: S.46, C.47, T.48, N.69, M.71, G.72, L.73, P.74, N.75, S.101, N.129, C.132, P.133, N.134, N.196, S.197 Ligands: FMN.30 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.48 Hydrogen bonds: B:N.69, B:N.69, B:M.71, B:G.72, B:N.129, B:N.134, B:N.196, B:N.196, B:S.197

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: I.173, R.240, R.241 Chain B: K.216, Q.217, F.219 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.216, A:R.241, A:R.241 Water bridges: B:Q.217, B:Q.217, B:Q.217 GOL.3: 4 residues within 4Å: Chain A: Y.60, M.71, Q.277 Ligands: CAC.21 6 PLIP interactions: 6 interactions with chain A Water bridges: A:G.22, A:G.22, A:G.22, A:S.26, A:R.59, A:Q.277 GOL.4: 2 residues within 4Å: Chain A: D.177, T.178 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.177, A:D.177, A:T.178, A:T.178, A:T.178 GOL.5: 5 residues within 4Å: Chain A: G.137, K.138, P.139 Chain B: I.173, A.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.137, A:K.138 Water bridges: A:V.135 GOL.6: 5 residues within 4Å: Chain A: F.63, V.203, I.204, Y.226 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.226 Water bridges: A:I.204, A:Y.226 GOL.7: 7 residues within 4Å: Chain A: V.12, A.14, Y.91, S.92, K.93, P.95 Ligands: EDO.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.12, A:A.14, A:S.92 Water bridges: A:V.12 GOL.24: 6 residues within 4Å: Chain A: K.216, Q.217, F.219 Chain B: I.173, R.240, R.241 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.241, B:R.241 Water bridges: A:Q.217, A:Q.217 GOL.25: 3 residues within 4Å: Chain B: Y.60, M.71, Q.277 8 PLIP interactions: 8 interactions with chain B Water bridges: B:G.22, B:G.22, B:G.22, B:S.26, B:E.57, B:R.59, B:Y.60, B:Q.277 GOL.26: 2 residues within 4Å: Chain B: D.177, T.178 5 PLIP interactions: 5 interactions with chain B Water bridges: B:D.177, B:D.177, B:T.178, B:T.178, B:T.178 GOL.27: 8 residues within 4Å: Chain A: Y.143, F.171, H.175 Chain B: Y.143, Y.170, F.171, D.172, H.175 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.171, B:D.172 GOL.28: 4 residues within 4Å: Chain B: L.6, N.7, E.304, R.307 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.7, B:R.307 Water bridges: B:R.307, B:R.307 GOL.29: 4 residues within 4Å: Chain B: C.33, A.36, S.37, P.281 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.38, B:P.281

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.8: 24 residues within 4Å: Chain A: A.20, A.21, G.22, V.23, K.45, S.46, Y.60, N.69, M.71, N.129, K.166, V.195, N.196, S.197, G.223, G.224, I.227, C.250, G.251, G.252, V.272, G.273, T.274 Ligands: 5LL.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.23, A:Y.60, A:Y.60 Hydrogen bonds: A:A.21, A:S.46, A:S.46, A:S.46, A:K.166, A:K.166, A:K.166, A:N.196, A:G.224, A:G.252, A:G.273, A:T.274 Water bridges: A:A.21, A:K.45, A:S.99, A:G.251, A:G.251, A:V.253, A:V.253 FMN.30: 23 residues within 4Å: Chain B: A.20, A.21, G.22, K.45, S.46, Y.60, N.69, M.71, N.129, K.166, V.195, N.196, S.197, G.223, G.224, I.227, C.250, G.251, G.252, V.272, G.273, T.274 Ligands: 5LL.23 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.60, B:Y.60 Hydrogen bonds: B:A.21, B:S.46, B:S.46, B:S.46, B:K.166, B:K.166, B:N.196, B:N.196, B:G.224, B:G.252, B:G.273, B:T.274 Water bridges: B:A.21, B:K.45, B:K.45, B:S.99, B:L.222, B:G.251, B:G.251, B:V.253, B:V.253

3 x NCO: COBALT HEXAMMINE(III)(Non-covalent)

NCO.9: 3 residues within 4Å: Chain A: K.298, Y.300 Ligands: EDO.37 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.298, A:Y.300 Water bridges: A:Y.300, A:Y.300 NCO.31: 5 residues within 4Å: Chain B: Q.277, E.278, E.279, G.280 Ligands: PEG.45 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.277, B:Q.277, B:Q.277 Water bridges: B:Q.277, B:E.278, B:E.278, B:E.278 NCO.32: 2 residues within 4Å: Chain B: D.205, S.208 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.208 Water bridges: B:E.207, B:E.207

23 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 3 residues within 4Å: Chain A: L.65, K.225 Chain B: L.65 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: E.279, R.286 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: Y.254, A.275, E.278, E.279, I.283, R.286 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: E.257, R.297, K.298 Chain B: A.206, E.207 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: R.113, A.116, A.158 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: S.210 Chain B: K.311, T.312, I.313 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: V.203, I.204 Chain B: L.228, L.232, L.261 Ligands: GOL.6 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: T.27, L.76 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: R.240, G.308, R.309, V.310, T.312 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: A.14, S.37, S.38, S.39, G.40, K.93, K.94 Ligands: GOL.7 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: E.28, E.29, R.32 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain A: A.206, E.207 Chain B: E.257, R.297, K.298 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain A: L.65 Chain B: L.65, K.225 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain B: R.240, G.308, R.309, V.310, T.312 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain B: L.76, G.77, F.78, D.79, F.80 Ligands: EDO.43 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain A: K.311 Chain B: E.207, S.208, E.209 Ligands: NCO.9 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain B: Y.254, A.275, E.278, E.279, I.283, R.286 Ligands: EDO.39 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain B: K.225, Y.254 Ligands: EDO.38 Ligand excluded by PLIP EDO.40: 2 residues within 4Å: Chain B: P.187, L.188 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain B: V.12, F.13, K.93, P.95 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain B: L.31, R.32, T.35, Y.84, L.88, H.89, D.90 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain B: P.51, D.79 Ligands: EDO.36 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain B: F.63, V.203, I.204 Ligand excluded by PLIP

2 x CAC: CACODYLATE ION(Non-covalent)(Non-functional Binders)

CAC.21: 4 residues within 4Å: Chain A: S.26, T.27, D.30 Ligands: GOL.3 5 PLIP interactions: 5 interactions with chain A Water bridges: A:L.24, A:Q.277, A:Q.277, A:Q.277, A:Q.277 CAC.22: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.279

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.45: 6 residues within 4Å: Chain B: L.24, E.279, G.280, P.281, G.282 Ligands: NCO.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rocha, J.R. et al., Exploring Trypanosoma cruzi Dihydroorotate Dehydrogenase Active Site Plasticity for the Discovery of Potent and Selective Inhibitors with Trypanocidal Activity. To be Published

Release Date

2016-10-19

Peptides

Dihydroorotate dehydrogenase (fumarate): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydroorotate dehydrogenase (fumarate)

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