SMTL ID : 4cm3.1

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 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x DTU: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTU.1: 7 residues within 4Å: Chain A: F.117, C.188, F.191, M.233, E.237, W.241 Ligands: KP2.3 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Water bridges: D:H.287, A:M.189 DTU.5: 3 residues within 4Å: Chain B: C.188, F.191, W.241 No protein-ligand interaction detected (PLIP) DTU.8: 4 residues within 4Å: Chain C: C.188, F.191, E.237, W.241 1 PLIP interactions: 1 interactions with chain C Water bridges: C:M.189 DTU.11: 6 residues within 4Å: Chain D: F.117, C.188, F.191, M.233, W.241 Ligands: KP2.13 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.287

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

NAP.2: 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: KP2.3 28 PLIP interactions: 28 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:L.228 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 pi-Stacking: A:H.55 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: KP2.7 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: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:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.9: 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: KP2.10 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:P.224 Hydrogen bonds: C:R.34, C:I.35, C:H.55, 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: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.12: 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: KP2.13 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: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:A.32, D:R.34, D:G.36, D:N.56, D:N.113, D:S.115 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

4 x KP2: 5-phenyl-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine(Non-covalent)

KP2.3: 10 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, Y.194, L.229, P.230, W.241 Ligands: DTU.1, NAP.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.117, A:F.117, A:L.229, A:P.230 Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:Y.194 pi-Stacking: A:F.117, A:F.117, A:W.241, A:W.241 KP2.7: 9 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, Y.194, L.229, P.230, W.241 Ligands: NAP.6 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 pi-Stacking: B:F.117, B:W.241, B:W.241 KP2.10: 9 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, Y.194, L.229, P.230, M.233 Ligands: NAP.9 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.117, C:F.117, C:L.229, C:P.230 Hydrogen bonds: C:R.34, C:S.115, C:S.115 Water bridges: C:R.34 pi-Stacking: C:F.117, C:F.117 KP2.13: 10 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, G.225, L.229, P.230 Ligands: DTU.11, NAP.12 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.117, D:L.229, D:P.230 Hydrogen bonds: D:R.34, D:S.115, D:S.115, D:Y.194 pi-Stacking: D:F.117, D:F.117

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

ACT.4: 3 residues within 4Å: Chain A: K.33, R.34, R.37 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.33 Hydrogen bonds: A:R.34 Salt bridges: A:R.37

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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