SMTL ID : 4cm4.1

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 1.81 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, A.116, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: 4NR.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.34, A:I.35, 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:L.228 Water bridges: A:K.33, A:R.34, A:G.36, A:H.55, A:H.55, A:S.57, A:N.113, A:S.115 Salt bridges: A:R.34, A:R.34 pi-Stacking: A:H.55 NAP.4: 27 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, A.116, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: 4NR.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: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:R.34, B:G.36, B:H.55, B:H.55, B:S.57, B:S.57, B:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.8: 27 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 Ligands: 4NR.9 26 PLIP interactions: 26 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:L.228 Water bridges: C:G.30, C:A.32, 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.10: 29 residues within 4Å: Chain D: 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, A.116, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: 4NR.11 26 PLIP interactions: 26 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:K.33, D:K.33, D:R.34, D:G.36, D:N.113, D:S.115 Salt bridges: D:R.34, D:R.34

4 x 4NR: 5-(4-FLUOROPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDINE-2,4-DIAMINE(Non-covalent)

4NR.2: 11 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, GOL.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.117, A:F.117, A:P.230 Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:Y.194 Water bridges: A:F.117 pi-Stacking: A:F.117 4NR.5: 10 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, Y.194, L.229, P.230, M.233, W.241 Ligands: NAP.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.117, B:L.229, B:P.230 Hydrogen bonds: B:R.34, B:S.115, B:S.115, B:Y.194 Water bridges: B:R.34, B:F.117 pi-Stacking: B:F.117, B:F.117 4NR.9: 11 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, Y.194, G.225, L.229, P.230, M.233, W.241 Ligands: NAP.8 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.117, C:P.230 Hydrogen bonds: C:R.34, C:S.115, C:S.115 Water bridges: C:R.34, C:L.228 pi-Stacking: C:F.117, C:F.117 4NR.11: 10 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, L.229, P.230, M.233, W.241 Ligands: NAP.10 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.117, D:F.117, D:P.230 Hydrogen bonds: D:R.34, D:S.115, D:S.115 Water bridges: D:R.34, D:F.117, D:L.228 pi-Stacking: D:F.117, D:F.117

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: C.188, P.230, M.233, W.241 Ligands: 4NR.2 No protein-ligand interaction detected (PLIP)

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

ACT.6: 4 residues within 4Å: Chain B: A.232, M.233, G.234, E.235 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.235 Water bridges: B:K.238, B:K.238 Salt bridges: B:K.238 ACT.7: 5 residues within 4Å: Chain B: A.65, N.69, A.76, V.77, V.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.78 Water bridges: B:D.66

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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