SMTL ID : 4clo.1

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 27 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 Ligands: XP0.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.34, A:I.35, A:H.55, A:H.55, A:N.56, A:N.56, A:S.57, A:D.82, A:L.83, 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:S.227 Water bridges: A:A.32, A:R.34, A:G.36, A:N.113, A:S.115 Salt bridges: A:R.34, A:R.34 NAP.3: 25 residues within 4Å: Chain B: 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: XP0.4 27 PLIP interactions: 27 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:N.113, B:S.115, B:S.115, B:S.115, B:Y.194, B:K.198, B:S.227, B:S.227 Water bridges: B:A.32, B:R.34, B:G.36, B:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 NAP.5: 25 residues within 4Å: Chain C: 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: XP0.6 24 PLIP interactions: 24 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:R.34, C:G.36, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 pi-Stacking: C:H.55 NAP.7: 26 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 Ligands: XP0.8 25 PLIP interactions: 25 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:S.227 Water bridges: D:R.34, D:G.36, D:N.113, D:S.115 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

4 x XP0: 5-(phenylethynyl)-4-(pyrrolidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-2-amine(Non-covalent)

XP0.2: 10 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, Y.194, L.229, P.230, M.233, W.241 Ligands: NAP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.117, A:L.229, A:P.230 Hydrogen bonds: A:S.115, A:S.115, A:Y.194, A:Y.194 pi-Stacking: A:F.117, A:W.241, A:W.241 XP0.4: 9 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, Y.194, L.229, P.230, W.241 Ligands: NAP.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.117, B:L.229, B:P.230 Hydrogen bonds: B:S.115, B:S.115, B:Y.194, B:Y.194 pi-Stacking: B:F.117, B:F.117, B:W.241, B:W.241 XP0.6: 11 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, Y.194, V.226, L.229, P.230, M.233, W.241 Ligands: NAP.5 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.117, C:V.226, C:L.229, C:P.230 Hydrogen bonds: C:S.115, C:S.115, C:Y.194 pi-Stacking: C:F.117, C:F.117, C:W.241, C:W.241 XP0.8: 11 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, V.226, L.229, P.230, M.233, W.241 Ligands: NAP.7 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.117, D:V.226, D:L.229, D:P.230 Hydrogen bonds: D:S.115, D:S.115, D:Y.194 pi-Stacking: D:F.117, D:W.241, D:W.241

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain D: L.228, L.229, E.251, A.252, S.253 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.229, D:L.229 Water bridges: D:R.242, D:E.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khalaf, A.I. et al., Structure-Based Design and Synthesis of Antiparasitic Pyrrolopyrimidines Targeting Pteridine Reductase 1. J.Med.Chem. (2014)

Release Date

2015-01-21

Peptides

PTERIDINE REDUCTASE 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PTERIDINE REDUCTASE 1

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