SMTL ID : 5ea9.1

Crystal Structure of Trypanosoma cruzi Dihydroorotate Dehydrogenase in Complex with Neq0130

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x 5LM: 5-[(E)-3-thiophen-2-ylprop-2-enylidene]-1,3-diazinane-2,4,6-trione(Covalent)

5LM.1: 17 residues within 4Å: Chain A: 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.9 9 PLIP interactions: 9 interactions with chain A 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 5LM.15: 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.22 9 PLIP interactions: 9 interactions with chain B 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

13 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 4 PLIP interactions: 2 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 GOL.3: 4 residues within 4Å: Chain A: F.63, V.203, I.204, D.205 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.205 Water bridges: B:E.257 GOL.4: 4 residues within 4Å: Chain A: Y.60, M.71, Q.277 Ligands: GOL.8 5 PLIP interactions: 5 interactions with chain A Water bridges: A:G.22, A:G.22, A:S.26, A:S.26, A:R.59 GOL.5: 2 residues within 4Å: Chain A: D.177, T.178 4 PLIP interactions: 4 interactions with chain A Water bridges: A:A.174, A:D.177, A:D.177, A:T.178 GOL.6: 4 residues within 4Å: Chain A: L.6, N.7, E.304, R.307 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.7, A:E.304, A:E.304, A:R.307, A:R.307 Water bridges: A:E.304 GOL.7: 2 residues within 4Å: Chain A: Y.239, P.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.239, A:P.243 Water bridges: A:Y.239, A:G.308 GOL.8: 5 residues within 4Å: Chain A: L.24, S.26, T.27, D.30 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.24, A:S.26 Water bridges: A:T.27, A:D.30, A:Q.277 GOL.16: 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, A:K.216, A:Q.217 GOL.17: 8 residues within 4Å: Chain A: Y.143, F.171, H.175 Chain B: Y.143, Y.170, F.171, D.172, H.175 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.171 GOL.18: 2 residues within 4Å: Chain B: D.177, T.178 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.177, B:D.177, B:T.178, B:T.178 GOL.19: 5 residues within 4Å: Chain A: I.173, A.174 Chain B: G.137, K.138, P.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.137, B:K.138 Water bridges: B:V.135 GOL.20: 1 residues within 4Å: Chain B: Y.60 5 PLIP interactions: 5 interactions with chain B Water bridges: B:G.22, B:G.22, B:S.26, B:R.59, B:Q.277 GOL.21: 5 residues within 4Å: Chain B: C.33, A.36, S.37, P.281, G.282 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.33 Water bridges: B:S.38

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.9: 23 residues within 4Å: Chain A: 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: 5LM.1 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: 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:N.196, A:N.196, A:G.224, A:G.252, A:G.273, A:T.274 Water bridges: A:A.21, A:K.45, A:K.45, A:K.45, A:S.99, A:L.222, A:G.251, A:G.251, A:V.253, A:V.253 FMN.22: 23 residues within 4Å: Chain B: 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, G.273, T.274 Ligands: 5LM.15 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:V.23, B:Y.60, B:Y.60 Hydrogen bonds: B:A.21, B:S.46, B:S.46, B:S.46, B:N.129, B:K.166, B:K.166, B:K.166, 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:K.45, B:S.99, B:G.251, B:G.251, B:V.253, B:V.253

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

EDO.10: 3 residues within 4Å: Chain A: L.65, K.225 Chain B: L.65 No protein-ligand interaction detected (PLIP) EDO.11: 6 residues within 4Å: Chain A: P.51, L.76, G.77, F.78, D.79, F.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.77, A:D.79, A:F.80 EDO.12: 6 residues within 4Å: Chain A: Y.254, A.275, E.278, E.279, I.283, R.286 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.279, A:R.286 EDO.13: 5 residues within 4Å: Chain A: V.12, A.14, K.93, K.94, P.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.12 Water bridges: A:A.14 EDO.14: 4 residues within 4Å: Chain A: L.24, E.279, G.280, P.281 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.279, A:G.280 EDO.25: 3 residues within 4Å: Chain A: L.65 Chain B: L.65, K.225 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.225 Water bridges: B:K.225 EDO.26: 5 residues within 4Å: Chain B: Y.254, A.275, E.278, E.279, R.286 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.279, B:R.286 EDO.27: 4 residues within 4Å: Chain B: R.113, A.116, P.117, A.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.113, B:R.113 EDO.28: 4 residues within 4Å: Chain B: F.63, V.203, I.204, D.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.205 EDO.29: 2 residues within 4Å: Chain B: T.27, L.76 No protein-ligand interaction detected (PLIP) EDO.30: 6 residues within 4Å: Chain B: R.32, T.35, Y.84, L.88, H.89, D.90 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.32, B:Y.84, B:Y.84

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

NCO.23: 4 residues within 4Å: Chain B: Q.277, E.278, E.279, G.280 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.277, B:Q.277, B:Q.277, B:E.278 NCO.24: 2 residues within 4Å: Chain B: D.205, S.208 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.208

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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