SMTL ID : 3jqf.1

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 1,3,5-triazine-2,4,6-triamine (AX2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: AX2.2, D1D.4 29 PLIP interactions: 29 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: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: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.10: 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: AX2.11, D1D.13 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:G.36, B:H.55, 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.14: 27 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, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: AX2.15, D1D.17 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:G.36, C:S.57, C:S.57, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 NAP.21: 28 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: AX2.22, D1D.24 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: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:G.30, D:R.34, 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 AX2: 1,3,5-triazine-2,4,6-triamine(Non-covalent)

AX2.2: 8 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, Y.194, P.230 Ligands: NAP.1, D1D.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:Y.194, A:Y.194 Water bridges: A:L.228 pi-Stacking: A:F.117 pi-Cation interactions: A:F.117 AX2.11: 7 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, Y.194 Ligands: NAP.10, D1D.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.34, B:S.115, B:S.115, B:Y.194, B:Y.194 Water bridges: B:L.228 pi-Stacking: B:F.117 pi-Cation interactions: B:F.117 AX2.15: 8 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, Y.194, P.230 Ligands: NAP.14, D1D.17 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.34, C:S.115, C:S.115, C:Y.194 Water bridges: C:L.228 pi-Stacking: C:F.117 pi-Cation interactions: C:F.117 AX2.22: 8 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, P.230 Ligands: NAP.21, D1D.24 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.34, D:S.115, D:S.115, D:Y.194, D:L.228 pi-Stacking: D:F.117 pi-Cation interactions: D:F.117

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

DTT.3: 6 residues within 4Å: Chain A: C.188, F.191, M.233, E.237, W.241 Ligands: D1D.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:E.237, A:E.237 Water bridges: A:M.189, D:H.287, D:H.287 DTT.9: 3 residues within 4Å: Chain A: E.235, K.238, R.242 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.238, A:R.242, A:R.242 Water bridges: A:E.235 DTT.12: 5 residues within 4Å: Chain B: C.188, F.191, E.237, W.241 Ligands: D1D.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.237 Water bridges: B:M.189, B:E.237 DTT.16: 6 residues within 4Å: Chain C: C.188, F.191, M.233, E.237, W.241 Ligands: D1D.17 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:M.189, B:H.287 DTT.23: 6 residues within 4Å: Chain D: C.188, F.191, M.233, E.237, W.241 Ligands: D1D.24 1 PLIP interactions: 1 interactions with chain D Water bridges: D:M.189

4 x D1D: (4S,5S)-1,2-DITHIANE-4,5-DIOL(Non-covalent)

D1D.4: 11 residues within 4Å: Chain A: F.117, D.181, M.183, C.188, G.225, V.226, L.229, W.241 Ligands: NAP.1, AX2.2, DTT.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.181 D1D.13: 10 residues within 4Å: Chain B: F.117, D.181, M.183, G.225, V.226, L.229, W.241 Ligands: NAP.10, AX2.11, DTT.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.181 D1D.17: 11 residues within 4Å: Chain C: F.117, D.181, M.183, C.188, G.225, V.226, P.230, W.241 Ligands: NAP.14, AX2.15, DTT.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.181 D1D.24: 10 residues within 4Å: Chain D: F.117, D.181, M.183, G.225, L.229, P.230, W.241 Ligands: NAP.21, AX2.22, DTT.23 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.181

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

ACT.5: 3 residues within 4Å: Chain A: K.33, R.34, R.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.34 ACT.6: 4 residues within 4Å: Chain A: Q.206, G.274, I.276 Chain B: K.278 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Water bridges: B:K.278, B:K.278, B:K.278, B:K.278, A:I.276 Salt bridges: B:K.278 Hydrophobic interactions: A:Q.206, A:I.276 ACT.7: 4 residues within 4Å: Chain A: K.278 Chain B: Q.206, G.274, I.276 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Water bridges: A:K.278, A:K.278, A:K.278, A:K.278 Salt bridges: A:K.278 Hydrophobic interactions: B:Q.206, B:I.276 Hydrogen bonds: B:Q.206 ACT.18: 3 residues within 4Å: Chain C: A.65, V.77, V.78 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.65 Hydrogen bonds: C:V.78 Water bridges: C:N.69 ACT.19: 4 residues within 4Å: Chain C: K.278 Chain D: Q.206, G.274, I.276 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.276 Hydrogen bonds: D:Q.206 Water bridges: C:K.278, C:K.278 Salt bridges: C:K.278 ACT.25: 4 residues within 4Å: Chain C: Q.206, G.274, I.276 Chain D: K.278 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Water bridges: D:K.278, D:K.278, D:K.278, D:K.278 Salt bridges: D:K.278 Hydrophobic interactions: C:Q.206, C:I.276 Hydrogen bonds: C:Q.206

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: L.228, R.250, E.251, S.253 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.250, A:E.251, A:E.251 Water bridges: A:R.242, A:E.251, A:E.251, A:S.253 GOL.20: 4 residues within 4Å: Chain C: Y.54, V.78, C.79, Q.80 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.54, C:Q.80 Water bridges: C:R.102

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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