SMTL ID : 3jq7.1

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6-phenylpteridine-2,4,7-triamine (DX2)

Coordinates

PDB Format Compare

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, 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: DX2.2 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:G.30, A:R.34, A:G.36, 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: 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: DX2.5, DTT.6 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:G.36, B:H.55, 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: DX2.9 22 PLIP interactions: 22 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:L.83, C:T.84, 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:A.32, C:G.36, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 NAP.10: 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: DX2.11 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: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 DX2: 6-phenylpteridine-2,4,7-triamine(Non-covalent)

DX2.2: 12 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, Y.194, V.226, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.226, A:L.229, A:P.230 Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:Y.194, A:Y.194, A:L.229 Water bridges: A:V.231 pi-Stacking: A:F.117, A:F.117, A:W.241, A:W.241 DX2.5: 11 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, Y.194, L.228, L.229, P.230, W.241 Ligands: NAP.4, DTT.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.229, B:P.230 Hydrogen bonds: B:R.34, B:S.115, B:S.115, B:Y.194, B:Y.194 pi-Stacking: B:F.117, B:F.117, B:W.241, B:W.241 DX2.9: 10 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, Y.194, V.226, L.228, L.229, P.230 Ligands: NAP.8 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:V.226, C:L.229 Hydrogen bonds: C:R.34, C:S.115, C:S.115, C:D.181, C:Y.194, C:L.229 pi-Stacking: C:F.117, C:F.117, C:W.241 DX2.11: 11 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.10 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: 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, D:W.241, D:W.241

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

ACT.3: 3 residues within 4Å: Chain A: K.33, R.34, R.37 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.33 Hydrogen bonds: A:R.34 ACT.7: 3 residues within 4Å: Chain B: Y.54, V.62, V.78 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.62 Hydrogen bonds: B:Y.54, B:Y.54 Water bridges: B:Q.80

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

DTT.6: 10 residues within 4Å: Chain B: F.117, D.181, M.183, C.188, Y.194, G.225, V.226, W.241 Ligands: NAP.4, DX2.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.181

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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