SMTL ID : 2wp5.1 (1 other biounit)

Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline inhibitor (DDD00065414)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 37 residues within 4Å: Chain A: I.13, G.14, G.16, S.17, G.18, V.37, D.38, V.39, A.49, A.50, G.53, T.54, C.55, V.58, G.59, C.60, K.63, G.128, W.129, G.130, A.162, T.163, G.164, F.201, I.202, F.206, R.290, R.293, G.329, D.330, M.336, L.337, T.338, P.339, A.341 Chain B: H.464, P.465 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.54, A:K.63, A:I.202, A:I.202, A:F.206 Hydrogen bonds: A:S.17, A:S.17, A:G.18, A:A.49, A:A.50, A:G.53, A:T.54, A:T.54, A:C.55, A:K.63, A:G.130, A:G.130, A:R.293, A:D.330, A:M.336, A:T.338, A:T.338, B:H.464 Water bridges: A:G.16, A:G.19, B:H.464 pi-Stacking: A:F.201, A:F.201 FAD.6: 37 residues within 4Å: Chain A: H.464, P.465 Chain B: I.13, G.14, A.15, G.16, S.17, G.18, V.37, D.38, V.39, A.49, A.50, G.53, T.54, C.55, V.58, G.59, C.60, K.63, G.128, W.129, G.130, A.162, T.163, G.164, F.201, I.202, R.290, R.293, G.329, D.330, M.336, L.337, T.338, P.339, A.341 28 PLIP interactions: 26 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.54, B:I.202 Hydrogen bonds: B:S.17, B:S.17, B:G.18, B:V.39, B:A.49, B:A.50, B:G.53, B:T.54, B:T.54, B:C.55, B:K.63, B:G.130, B:G.130, B:R.293, B:D.330, B:M.336, B:T.338, B:T.338, B:T.338, A:H.464 Water bridges: B:G.16, B:G.19, B:S.165, A:H.464 pi-Stacking: B:F.201, B:F.201

2 x WP5: METHYL [(4S)-6-BROMO-2-METHYL-4-PHENYLQUINAZOLIN-3(4H)-YL]ACETATE(Non-covalent)

WP5.2: 9 residues within 4Å: Chain A: G.16, S.17, L.20, E.21, W.24, G.52, Y.113, M.116, F.117 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.20, A:L.20, A:L.20, A:E.21, A:W.24, A:W.24, A:W.24, A:Y.113, A:M.116, A:F.117 pi-Stacking: A:Y.113 Halogen bonds: A:G.52 WP5.7: 10 residues within 4Å: Chain B: S.17, L.20, E.21, W.24, G.52, V.56, Y.113, M.116, F.117, L.123 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.20, B:L.20, B:E.21, B:W.24, B:W.24, B:W.24, B:Y.113, B:Y.113, B:M.116, B:F.117, B:L.123 Halogen bonds: B:G.52

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

CL.3: 2 residues within 4Å: Chain A: Y.224, R.225 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: N.94, W.95, K.96, P.190 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: G.198, Y.224, R.225, I.288 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: N.94, W.95, K.96 Ligand excluded by PLIP

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

NA.5: 3 residues within 4Å: Chain A: Y.458, T.460, C.472 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.458 NA.10: 5 residues within 4Å: Chain B: Y.458, T.460, I.461, G.462, C.472 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.458, B:G.462 NA.11: 4 residues within 4Å: Chain B: F.117, T.120, L.123, D.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.123, B:L.123, B:D.124

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.12: 8 residues within 4Å: Chain B: P.167, S.181, I.202, M.286, A.287, I.288, G.289, R.290 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.167, B:I.202, B:R.290 Hydrogen bonds: B:S.181, B:R.290, B:R.290 MPD.13: 5 residues within 4Å: Chain B: T.363, R.364, G.379, L.380, L.428 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.364, B:L.380 Hydrogen bonds: B:R.364, B:V.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patterson, S. et al., Dihydroquinazolines as a Novel Class of Trypanosoma Brucei Trypanothione Reductase Inhibitors: Discovery, Synthesis, and Characterization of Their Binding Mode by Protein Crystallography. J.Med.Chem. (2011)

Release Date

2010-10-13

Peptides

TRYPANOTHIONE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

TRYPANOTHIONE REDUCTASE

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