SMTL ID : 3jqd.1

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-4-oxo-6-phenyl-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (DX7)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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, 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: DX7.2 26 PLIP interactions: 26 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: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:A.32, A:K.33, A:G.36, 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: 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: DX7.5 25 PLIP interactions: 25 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:L.83, B:T.84, B:N.113, B:S.115, B:S.115, B:S.115, B:K.198, B:S.227, B:L.228 Water bridges: 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.6: 26 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, L.228 Ligands: DX7.7 30 PLIP interactions: 30 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:D.82, C:L.83, C:T.84, C:T.84, C:N.113, C:S.115, C:S.115, C:S.115, C:Y.194, C:K.198, C:S.227, C:L.228 Water bridges: C:R.34, C:G.36, C:H.55, C:H.55, C:S.57, C:S.57, C:N.113 Salt bridges: C:R.34, C:R.34 pi-Stacking: C:H.55 NAP.8: 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: DX7.9 28 PLIP interactions: 28 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: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:G.30, 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 DX7: 2-amino-4-oxo-6-phenyl-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile(Non-covalent)

DX7.2: 11 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, M.183, C.188, Y.194, G.225, L.229, P.230 Ligands: NAP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:Y.194 pi-Stacking: A:F.117, A:F.117 DX7.5: 12 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, M.183, C.188, Y.194, G.225, V.226, L.229, P.230 Ligands: NAP.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.226 Hydrogen bonds: B:R.34, B:S.115, B:D.181 pi-Stacking: B:F.117, B:F.117 DX7.7: 10 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, M.183, Y.194, G.225, V.226, P.230 Ligands: NAP.6 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:M.183, C:V.226 Hydrogen bonds: C:R.34, C:S.115, C:S.115, C:D.181, C:Y.194 pi-Stacking: C:F.117, C:F.117 DX7.9: 12 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, M.183, C.188, Y.194, G.225, V.226, L.229, P.230 Ligands: NAP.8 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:M.183, D:V.226 Hydrogen bonds: D:R.34, D:S.115, D:S.115, D:D.181, D:Y.194, D:Y.194 pi-Stacking: D:F.117, D:F.117

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

ACT.3: 4 residues within 4Å: Chain A: F.117, C.188, F.191, M.233 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.117 Water bridges: A:E.237, A:E.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tulloch, L.B. et al., Structure-based design of pteridine reductase inhibitors targeting african sleeping sickness and the leishmaniases. J.Med.Chem. (2010)

Release Date

2009-12-08

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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