SMTL ID : 3bmo.1

Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor (Compound AX4)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

ACT.1: 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.2: 5 residues within 4Å: Chain A: K.278 Chain B: Q.206, G.274, I.276 Ligands: NA.4 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.206, B:I.276 Hydrogen bonds: B:Q.206 Salt bridges: A:K.278 ACT.3: 3 residues within 4Å: Chain A: E.235, K.238, R.242 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.238, A:R.242 Salt bridges: A:K.238, A:R.242 ACT.10: 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 Salt bridges: B:K.278 Hydrophobic interactions: A:Q.206, A:I.276 Hydrogen bonds: A:Q.206 ACT.17: 4 residues within 4Å: Chain C: K.278 Chain D: Q.206, G.274, I.276 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Q.206, D:I.276 Hydrogen bonds: D:Q.206 Water bridges: C:K.278, C:K.278 Salt bridges: C:K.278 ACT.18: 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 ACT.23: 4 residues within 4Å: Chain C: Q.206, G.274, I.276 Chain D: K.278 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Q.206, C:I.276 Hydrogen bonds: C:Q.206 Water bridges: D:K.278, D:K.278 Salt bridges: D:K.278

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: K.278, S.284 Ligands: ACT.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.278, A:S.284, A:S.284

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

NAP.5: 29 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, L.228 Ligands: AX4.6, D1D.8 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: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:K.33, A:R.34, A:G.36, A:H.55, A:H.55, A:S.57, A:N.113 Salt bridges: A:R.34, A:R.34 pi-Stacking: A:H.55 NAP.11: 29 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: AX4.12, D1D.14, GOL.15 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: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:R.34, B:G.36, B:H.55, B:H.55, B:S.57, B:N.113 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.19: 28 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: AX4.20, D1D.22 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:H.55, 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:G.30, C:A.32, C:R.34, C:G.36, C:N.113 Salt bridges: C:R.34, C:R.34 NAP.24: 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, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: AX4.25, D1D.27 27 PLIP interactions: 27 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:K.33, D:K.33, D:K.33, D:R.34, D:G.36, D:N.56, D:N.56, D:N.113 Salt bridges: D:R.34, D:R.34

4 x AX4: 6-[(4-methylphenyl)sulfanyl]pyrimidine-2,4-diamine(Non-covalent)

AX4.6: 13 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, Y.194, V.226, L.228, L.229, P.230, W.241 Ligands: NAP.5, DTT.7, D1D.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.117, A:V.226, A:L.229, A:P.230, A:W.241 Hydrogen bonds: A:S.115, A:S.115, A:Y.194, A:Y.194 pi-Stacking: A:F.117 AX4.12: 13 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.11, DTT.13, D1D.14, GOL.15 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 AX4.20: 12 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, Y.194, L.228, L.229, P.230, W.241 Ligands: NAP.19, DTT.21, D1D.22 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.117, C:L.229, C:P.230, C:W.241 Hydrogen bonds: C:S.115, C:S.115, C:Y.194 Water bridges: C:R.34 pi-Stacking: C:F.117 AX4.25: 13 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, V.226, L.228, L.229, P.230, W.241 Ligands: NAP.24, DTT.26, D1D.27 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.117, D:V.226, D:L.229, D:P.230, D:W.241 Hydrogen bonds: D:S.115, D:S.115, D:Y.194 Water bridges: D:R.34 pi-Stacking: D:F.117

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

DTT.7: 7 residues within 4Å: Chain A: C.188, F.191, M.233, W.241 Chain D: H.287 Ligands: AX4.6, D1D.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.189 DTT.13: 6 residues within 4Å: Chain B: C.188, F.191, E.237, W.241 Chain C: H.287 Ligands: AX4.12 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:M.189, C:H.287 DTT.21: 8 residues within 4Å: Chain B: H.287 Chain C: C.188, F.191, M.233, E.237, W.241 Ligands: AX4.20, D1D.22 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:H.287, C:M.189 DTT.26: 7 residues within 4Å: Chain A: H.287 Chain D: C.188, M.233, E.237, W.241 Ligands: AX4.25, D1D.27 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Water bridges: D:M.189, A:H.287

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

D1D.8: 9 residues within 4Å: Chain A: F.117, D.181, M.183, G.225, V.226, W.241 Ligands: NAP.5, AX4.6, DTT.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.225 D1D.14: 7 residues within 4Å: Chain B: M.183, C.188, G.225, W.241 Ligands: NAP.11, AX4.12, GOL.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.225 D1D.22: 9 residues within 4Å: Chain C: F.117, D.181, M.183, G.225, P.230, W.241 Ligands: NAP.19, AX4.20, DTT.21 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.225 D1D.27: 9 residues within 4Å: Chain D: F.117, D.181, M.183, G.225, V.226, W.241 Ligands: NAP.24, AX4.25, DTT.26 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.225

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: L.228, R.250, E.251, S.253 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.250, A:R.250, A:E.251 Water bridges: A:E.251, A:S.253 GOL.15: 9 residues within 4Å: Chain B: D.181, M.183, C.188, Y.194, G.225, W.241 Ligands: NAP.11, AX4.12, D1D.14 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.181, B:M.183 GOL.16: 4 residues within 4Å: Chain B: D.66, A.76, V.77, V.78 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.66, B:V.78 Water bridges: B:D.66, B:D.66

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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