SMTL ID : 6hnc.1

Trypanosoma brucei PTR1 in complex with cycloguanil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 28 residues within 4Å: Chain A: G.30, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: 1CY.2, GOL.4 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.34, A:I.35, A:H.55, A:N.56, A:S.57, A:D.82, A:D.82, A:L.83, A:T.84, A:N.113, A:S.115, A:S.115, A:S.115, A:K.198, A:S.227, A:L.228 Water bridges: A:G.30, A:A.32, A:A.32, A:R.34, A:G.36, A:N.113 Salt bridges: A:R.34, A:R.34 NAP.6: 27 residues within 4Å: Chain B: K.33, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: 1CY.7 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:P.224 Hydrogen bonds: B:R.34, B:I.35, B:H.55, B:H.55, B:N.56, B:N.56, B:S.57, B:D.82, B:L.83, B:T.84, B:T.84, B:N.113, B:S.115, B:S.115, B:S.115, B:Y.194, B:K.198, B:S.227, B:L.228 Water bridges: B:G.30, B:R.34, B:G.36, B:S.57, B:S.57, B:N.113 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.13: 26 residues within 4Å: Chain C: G.30, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:P.224 Hydrogen bonds: C:R.34, C:I.35, C:H.55, C:N.56, C:N.56, C:S.57, C:D.82, C:L.83, C:T.84, C:N.113, C:S.115, C:S.115, C:S.115, C:K.198, C:G.225, C:S.227 Water bridges: C:A.32, C:G.36, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 NAP.17: 27 residues within 4Å: Chain D: G.30, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: 1CY.18 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:P.224 Hydrogen bonds: D:R.34, D:I.35, D:H.55, D:H.55, D:N.56, D:N.56, D:S.57, D:D.82, D:D.82, D:L.83, D:T.84, D:T.84, D:N.113, D:S.115, D:S.115, D:S.115, D:Y.194, D:K.198, D:S.227, D:L.228 Water bridges: D:A.32, D:A.32, D:G.36, D:S.57, D:N.113 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

3 x 1CY: 1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine(Non-covalent)

1CY.2: 10 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, Y.194, L.228, L.229, W.241 Ligands: NAP.1, GOL.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.117, A:F.117 Hydrogen bonds: A:S.115, A:S.115, A:Y.194 pi-Cation interactions: A:F.117 1CY.7: 10 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, Y.194, L.228, L.229, P.230, W.241 Ligands: NAP.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.117 Hydrogen bonds: B:S.115, B:Y.194, B:Y.194 pi-Stacking: B:F.117 pi-Cation interactions: B:F.117 1CY.18: 8 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, L.229, W.241 Ligands: NAP.17 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.117, D:F.117, D:F.117 Hydrogen bonds: D:S.115, D:S.115, D:Y.194, D:Y.194 pi-Cation interactions: D:F.117

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

ACT.3: 4 residues within 4Å: Chain A: K.278 Chain C: Q.206, G.274, I.276 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.276 Hydrogen bonds: C:Q.206 Water bridges: A:K.278, A:K.278 Salt bridges: A:K.278 ACT.8: 3 residues within 4Å: Chain B: K.33, R.34, R.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.34 Salt bridges: B:R.37 ACT.14: 2 residues within 4Å: Chain C: V.77, V.78 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.78 Water bridges: C:N.69 ACT.15: 4 residues within 4Å: Chain C: R.243, K.244, V.245, P.246 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.243

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: S.115, A.116, F.117 Ligands: NAP.1, 1CY.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.115, A:F.117, A:F.117 GOL.9: 3 residues within 4Å: Chain B: E.235, K.238, R.242 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.238, B:R.242, B:R.242 Water bridges: B:E.235, B:E.235 GOL.10: 4 residues within 4Å: Chain B: L.228, R.250, E.251, S.253 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.250, B:E.251 Water bridges: B:R.250, B:E.251, B:E.251, B:S.253 GOL.11: 8 residues within 4Å: Chain B: N.85, V.140, A.141 Chain C: N.85, V.140, A.141, G.145, I.149 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Water bridges: C:E.137, C:E.137, B:A.141 Hydrogen bonds: B:N.85 GOL.16: 4 residues within 4Å: Chain C: Y.54, V.78, C.79, Q.80 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.54, C:Q.80 Water bridges: C:S.99

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 4 residues within 4Å: Chain A: Q.206, G.274, I.276 Chain C: K.278 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.206, C:K.278 DMS.12: 4 residues within 4Å: Chain B: K.278 Chain D: Q.206, G.274, I.276 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.278, D:Q.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Landi, G. et al., Structural Insights into the Development of Cycloguanil Derivatives asTrypanosoma bruceiPteridine-Reductase-1 Inhibitors. Acs Infect Dis. (2019)

Release Date

2019-05-08

Peptides

Pteridine reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pteridine reductase

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