SMTL ID : 3bmq.1

Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor (Compound AX5)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 26 residues within 4Å: Chain A: 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, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: AX5.2, DTT.3 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:R.34, 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.5: 27 residues within 4Å: Chain B: 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: AX5.6, GOL.7 29 PLIP interactions: 29 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: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.56, B:N.56, B:S.57, B:N.113 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, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: AX5.10, GOL.12 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: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:A.32, C:R.34, C:G.36, C:S.57, C:N.113 Salt bridges: C:R.34, C:R.34 pi-Stacking: C:H.55 NAP.13: 26 residues within 4Å: Chain D: 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, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: AX5.14, DTT.15 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: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.56, D:S.57, D:T.84, D:N.113 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

4 x AX5: 6-(benzylsulfanyl)pyrimidine-2,4-diamine(Non-covalent)

AX5.2: 12 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, Y.194, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.1, DTT.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.117, A:L.229, A:P.230 Hydrogen bonds: A:S.115, A:S.115, A:Y.194, A:Y.194 Water bridges: A:R.34 pi-Stacking: A:F.117, A:W.241 AX5.6: 11 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, Y.194, L.228, L.229, P.230, M.233 Ligands: NAP.5, GOL.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.117, B:L.229, B:P.230 Hydrogen bonds: B:S.115, B:S.115, B:Y.194, B:Y.194 pi-Stacking: B:F.117 AX5.10: 13 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, Y.194, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.9, GOL.11, GOL.12 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.117, C:F.117, C:L.229, C:P.230 Hydrogen bonds: C:S.115, C:Y.194 Water bridges: C:R.34 pi-Stacking: C:F.117, C:W.241 AX5.14: 13 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, V.226, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.13, DTT.15 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.117, D:F.117, D:V.226, D:L.229, D:P.230 Hydrogen bonds: D:S.115, D:S.115, D:Y.194 pi-Stacking: D:F.117, D:W.241

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

DTT.3: 9 residues within 4Å: Chain A: D.181, M.183, C.188, Y.194, G.225, W.241 Chain D: H.287 Ligands: NAP.1, AX5.2 No protein-ligand interaction detected (PLIP) DTT.15: 9 residues within 4Å: Chain D: F.117, D.181, M.183, C.188, Y.194, G.225, W.241 Ligands: NAP.13, AX5.14 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.181 Water bridges: D:D.181, D:D.181, D:M.183

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

ACT.4: 4 residues within 4Å: Chain B: A.232, M.233, G.234, E.235 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.235 Water bridges: B:K.238 Salt bridges: B:K.238 ACT.8: 2 residues within 4Å: Chain C: V.77, V.78 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.78 Water bridges: C:N.69

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain B: F.117, D.181, M.183, Y.194, G.225, W.241 Ligands: NAP.5, AX5.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.225 Water bridges: B:D.181, B:D.181 GOL.11: 10 residues within 4Å: Chain B: H.287 Chain C: M.183, Q.186, P.187, C.188, G.225, V.226, W.241 Ligands: AX5.10, GOL.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.186, C:C.188 GOL.12: 8 residues within 4Å: Chain C: F.117, D.181, C.188, Y.194, G.225 Ligands: NAP.9, AX5.10, GOL.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.181, C:G.225 Water bridges: C:C.188

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

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