SMTL ID : 3mcv.1

Structure of PTR1 from Trypanosoma brucei in ternary complex with 2,4-diamino-5-[2-(2,5-dimethoxyphenyl)ethyl]thieno[2,3-d]-pyrimidine and NADP+

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: 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: MCV.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:R.34, 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 NAP.4: 27 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: MCV.5 30 PLIP interactions: 30 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.30, B:A.32, B:G.36, B:H.55, 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: MCV.9 24 PLIP interactions: 24 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:G.36, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 pi-Stacking: C:H.55 NAP.10: 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: MCV.11 24 PLIP interactions: 24 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

4 x MCV: 5-[2-(2,5-dimethoxyphenyl)ethyl]thieno[2,3-d]pyrimidine-2,4-diamine(Non-covalent)

MCV.2: 14 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, C.188, F.191, Y.194, G.225, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.117, A:L.229, A:P.230, A:W.241 Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:Y.194 Water bridges: A:R.34 pi-Stacking: A:F.117, A:F.117 MCV.5: 14 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, C.188, Y.194, G.225, V.226, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.117, B:L.229, B:W.241 Hydrogen bonds: B:R.34, B:S.115, B:Y.194 Water bridges: B:R.34 pi-Stacking: B:F.117, B:F.117 MCV.9: 15 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, C.188, F.191, Y.194, G.225, V.226, L.229, P.230, M.233, E.237, W.241 Ligands: NAP.8 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.117, C:L.229, C:W.241 Hydrogen bonds: C:R.34, C:S.115, C:S.115, C:L.228 pi-Stacking: C:F.117, C:F.117 MCV.11: 15 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, C.188, Y.194, G.225, V.226, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.10, ACT.12 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.117, D:L.229, D:W.241 Hydrogen bonds: D:R.34, D:S.115, D:S.115, D:L.228 pi-Stacking: D:F.117, D:F.117

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

ACT.3: 3 residues within 4Å: Chain A: R.242, R.250, E.251 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.235 Salt bridges: A:R.242, A:R.250 ACT.6: 4 residues within 4Å: Chain B: A.232, M.233, G.234, E.235 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.235 Water bridges: B:M.233, B:K.238, B:K.238, B:K.238 Salt bridges: B:K.238 ACT.7: 2 residues within 4Å: Chain B: Y.54, V.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.54, B:Y.54 ACT.12: 6 residues within 4Å: Chain A: H.287 Chain D: C.188, M.189, K.240, W.241 Ligands: MCV.11 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:W.241 Hydrogen bonds: D:M.189 Salt bridges: A:H.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dawson, A. et al., High-resolution structures of Trypanosoma brucei pteridine reductase ligand complexes inform on the placement of new molecular entities in the active site of a potential drug target. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-06-02

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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