SMTL ID : 3bmn.1

Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor (Compound AX3)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 29 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: AX3.2, GOL.3 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:H.55, 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:G.36, A:N.56, A:N.113 Salt bridges: A:R.34, A:R.34 pi-Stacking: A:H.55 NAP.6: 28 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: AX3.7, GOL.8 28 PLIP interactions: 28 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:L.83, B:T.84, 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:S.57, B:N.113, B:N.113, B:L.179 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.9: 28 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: AX3.10, GOL.12 23 PLIP interactions: 23 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: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 Salt bridges: C:R.34, C:R.34 pi-Stacking: C:H.55 NAP.14: 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, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: AX3.15, GOL.18 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:L.228 Water bridges: D:A.32, D:H.55, D:N.113, D:N.113 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

4 x AX3: N~2~-cyclopropyl-1,3,5-triazine-2,4,6-triamine(Non-covalent)

AX3.2: 8 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, Y.194, P.230 Ligands: NAP.1, GOL.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.117, A:P.230 Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:D.181, A:Y.194, A:Y.194 pi-Stacking: A:F.117 pi-Cation interactions: A:F.117 AX3.7: 10 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, Y.194, L.228, L.229, P.230 Ligands: NAP.6, GOL.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.117, B:P.230 Hydrogen bonds: B:S.115, B:S.115, B:Y.194, B:Y.194 pi-Stacking: B:F.117 pi-Cation interactions: B:F.117 AX3.10: 9 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, Y.194, L.228, P.230 Ligands: NAP.9, GOL.12 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.34, C:S.115, C:S.115, C:D.181, C:Y.194 Water bridges: C:R.34 pi-Stacking: C:F.117 pi-Cation interactions: C:F.117 AX3.15: 8 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, P.230 Ligands: NAP.14, GOL.18 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.115, D:S.115, D:Y.194 pi-Stacking: D:F.117 pi-Cation interactions: D:F.117

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: D.181, C.188, G.225, W.241 Ligands: NAP.1, AX3.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.181 GOL.4: 8 residues within 4Å: Chain A: N.85, S.86, N.87, E.137 Chain C: N.85, S.86, N.87, A.141 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:N.85, A:S.86, C:N.85, C:N.87 Water bridges: A:N.87, C:A.141 GOL.5: 4 residues within 4Å: Chain A: D.185, K.278, S.284, L.285 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.185, A:K.278, A:S.284 Water bridges: A:D.185 GOL.8: 6 residues within 4Å: Chain B: F.117, G.225, L.229, W.241 Ligands: NAP.6, AX3.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.241 Water bridges: B:D.181, B:G.225 GOL.12: 7 residues within 4Å: Chain C: F.117, D.181, G.225, V.226, W.241 Ligands: NAP.9, AX3.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.181, C:W.241 GOL.18: 6 residues within 4Å: Chain D: G.225, L.229, M.233, W.241 Ligands: NAP.14, AX3.15 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:W.241 Water bridges: D:D.181, D:D.181, D:G.225

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 2 residues within 4Å: Chain C: I.276, K.278 No protein-ligand interaction detected (PLIP) EDO.16: 5 residues within 4Å: Chain D: A.182, M.183, V.184, D.185, Q.186 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.185, D:Q.186, D:Q.186 EDO.17: 9 residues within 4Å: Chain B: P.187, C.188, M.189, A.190, F.191, S.192 Chain D: S.207, L.210, E.211 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.190, B:F.191, B:F.191 Water bridges: B:L.122

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

ACT.13: 4 residues within 4Å: Chain C: Q.206, G.274, I.276 Chain D: K.278 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.276 Hydrogen bonds: C:Q.206 Water bridges: D:K.278 Salt bridges: D:K.278

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

2008-12-16

Peptides

Pteridine reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pteridine reductase

Related Entries With Identical Sequence