SMTL ID : 5k6a.1

Trypanosoma brucei Pteridine reductase 1 (PTR1) in complex with compound 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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, 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: 6QT.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:R.34, A:I.35, A:H.55, A:H.55, A:N.56, A:N.56, A:S.57, A:L.83, A:T.84, A:T.84, A:T.84, A:N.113, A:S.115, A:S.115, A:S.115, A:Y.194, A:K.198, A:S.227, A:L.228 Water bridges: A:G.30, A:R.34, A:G.36, A:S.57, A:S.57, A:N.113, A:N.147 Salt bridges: A:R.34, A:R.34 pi-Stacking: A:H.55 NAP.4: 27 residues within 4Å: Chain B: 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: 6QT.5 31 PLIP interactions: 31 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: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:A.32, B:A.32, 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.6: 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 Ligands: 6QT.7 21 PLIP interactions: 21 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:S.227, C:S.227 Water bridges: C:G.36, C:N.113 Salt bridges: C:R.34, C:R.34 NAP.9: 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: 6QT.10 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:P.224 Hydrogen bonds: D:R.34, D:I.35, 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:N.113, D:S.115, D:S.115, D:S.115, D:K.198, D:S.227, D:L.228 Water bridges: D:G.30, D:A.32, D:A.32, D:G.36, D:N.113, D:N.147 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

4 x 6QT: (2~{R})-2-(3-hydroxyphenyl)-6-oxidanyl-2,3-dihydrochromen-4-one(Non-covalent)

6QT.2: 12 residues within 4Å: Chain A: R.34, S.115, F.117, M.183, Y.194, G.225, V.226, L.228, L.229, P.230, W.241 Ligands: NAP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.117, A:Y.194, A:V.226, A:L.229 Hydrogen bonds: A:R.34, A:S.115, A:G.225 Water bridges: A:F.117 pi-Stacking: A:F.117, A:W.241, A:W.241 6QT.5: 11 residues within 4Å: Chain B: R.34, S.115, F.117, M.183, Y.194, G.225, L.228, L.229, P.230, W.241 Ligands: NAP.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.117, B:Y.194, B:L.229 Hydrogen bonds: B:R.34, B:S.115, B:G.225 Water bridges: B:S.115, B:F.117 pi-Stacking: B:F.117, B:W.241, B:W.241 6QT.7: 8 residues within 4Å: Chain C: R.34, S.115, F.117, M.183, Y.194, V.226, W.241 Ligands: NAP.6 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.117, C:Y.194, C:V.226 Hydrogen bonds: C:R.34, C:S.115, C:G.225 Water bridges: C:F.117 pi-Stacking: C:F.117, C:W.241, C:W.241 6QT.10: 12 residues within 4Å: Chain D: R.34, S.115, F.117, M.183, Y.194, G.225, V.226, L.228, L.229, P.230, W.241 Ligands: NAP.9 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.117, D:Y.194, D:V.226 Hydrogen bonds: D:R.34, D:S.115, D:G.225 Water bridges: D:S.115, D:F.117 pi-Stacking: D:F.117, D:W.241, D:W.241

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

ACT.3: 3 residues within 4Å: Chain A: K.33, R.34, R.37 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.33 Hydrogen bonds: A:R.34 ACT.8: 2 residues within 4Å: Chain C: V.77, V.78 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Di Pisa, F. et al., Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity. Molecules (2017)

Release Date

2017-03-22

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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