SMTL ID : 3jq6.1

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6,7-bis(1-methylethyl)pteridine-2,4-diamine (DX1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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: DX1.2 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: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:G.36, A:H.55, A:H.55, A:S.57, 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: 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: DX1.5 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: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:K.198, B:S.227, B:S.227 Water bridges: B:G.36, B:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.7: 27 residues within 4Å: Chain C: 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: DX1.8 30 PLIP interactions: 30 interactions with chain C 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:T.84, C:N.113, C:S.115, C:S.115, C:S.115, C:Y.194, C:K.198, C:S.227, C:S.227 Water bridges: C:A.32, C:K.33, C:R.34, C:G.36, C:H.53, C:H.55, C:H.55, C:N.113 Salt bridges: C:K.33, C:R.34, C:R.34 pi-Stacking: C:H.55 NAP.12: 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: DX1.10 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:L.83, D:N.113, D:S.115, D:S.115, D:S.115, D:K.198, D:S.227, D:S.227 Water bridges: D:G.30, D:G.36, D:S.57, D:S.57, D:N.113, D:S.115 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

4 x DX1: 6,7-bis(1-methylethyl)pteridine-2,4-diamine(Non-covalent)

DX1.2: 11 residues within 4Å: Chain A: S.115, F.117, D.181, Y.194, G.225, V.226, S.227, L.229, P.230 Ligands: NAP.1, DTT.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.117, A:V.226, A:L.229 Hydrogen bonds: A:S.115, A:Y.194, A:Y.194 pi-Stacking: A:F.117, A:F.117 DX1.5: 9 residues within 4Å: Chain B: S.115, F.117, D.181, Y.194, S.227, L.228, L.229 Ligands: NAP.4, DTT.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.229 Hydrogen bonds: B:S.115, B:Y.194 pi-Stacking: B:F.117, B:F.117 DX1.8: 12 residues within 4Å: Chain C: S.115, F.117, D.181, Y.194, V.226, S.227, L.228, P.230, M.233, W.241 Ligands: NAP.7, DTT.9 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.117, C:V.226, C:W.241 Hydrogen bonds: C:S.115, C:S.115, C:Y.194, C:Y.194 pi-Stacking: C:F.117, C:F.117 DX1.10: 13 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, G.225, V.226, S.227, L.228, L.229, P.230 Ligands: DTT.11, NAP.12 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.117, D:L.229 Hydrogen bonds: D:S.115, D:S.115, D:Y.194 pi-Stacking: D:F.117, D:F.117

4 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.3: 4 residues within 4Å: Chain A: C.188, F.191, W.241 Ligands: DX1.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.189, A:E.237 DTT.6: 5 residues within 4Å: Chain B: C.188, E.237, W.241 Chain C: H.287 Ligands: DX1.5 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:H.287, B:M.189 DTT.9: 5 residues within 4Å: Chain B: H.287 Chain C: C.188, F.191, W.241 Ligands: DX1.8 1 PLIP interactions: 1 interactions with chain C Water bridges: C:M.189 DTT.11: 4 residues within 4Å: Chain D: C.188, E.237, W.241 Ligands: DX1.10 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.241 Water bridges: D:M.189

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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