SMTL ID : 4cma.1

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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, 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 Ligands: M2N.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: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:S.227 Water bridges: A:R.34, A:R.34, A:G.36, A:H.55, A:H.55, 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: 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 Ligands: M2N.6 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: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:S.227 Water bridges: B:A.32, B:A.32, B:R.34, 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, 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, Y.194, K.198, P.224, G.225, V.226, S.227 Ligands: M2N.9 29 PLIP interactions: 29 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:N.56, C:S.57, C:D.82, 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 Water bridges: C:G.30, C:K.33, C:R.34, C:S.57, C:S.57, C:N.113, C:S.115 Salt bridges: C:K.33, C:R.34, C:R.34 pi-Stacking: C:H.55 NAP.12: 26 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, Y.194, K.198, P.224, G.225, V.226, S.227 Ligands: M2N.13 26 PLIP interactions: 26 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:L.83, D:T.84, D:T.84, D:N.113, D:S.115, D:S.115, D:S.115, D:K.198, D:S.227, D:S.227 Water bridges: 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 M2N: 5,6-diphenyl-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine(Non-covalent)

M2N.2: 11 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, M.183, C.188, Y.194, G.225, V.226, L.229 Ligands: NAP.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.117, A:F.117, A:M.183, A:Y.194, A:V.226, A:L.229 Hydrogen bonds: A:R.34, A:S.115, A:Y.194, A:Y.194 Water bridges: A:R.34 pi-Stacking: A:F.117, A:F.117 M2N.6: 11 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, M.183, C.188, Y.194, G.225, V.226, L.229 Ligands: NAP.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.117, B:F.117, B:M.183, B:V.226, B:L.229 Hydrogen bonds: B:R.34, B:S.115, B:S.115, B:Y.194, B:Y.194 Water bridges: B:R.34 pi-Stacking: B:F.117, B:F.117 M2N.9: 12 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, M.183, C.188, Y.194, G.225, V.226, L.229, M.233 Ligands: NAP.8 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.117, C:F.117, C:M.183, C:Y.194, C:V.226, C:L.229 Hydrogen bonds: C:R.34, C:S.115, C:S.115, C:Y.194 Water bridges: C:R.34 pi-Stacking: C:F.117, C:F.117, C:W.241 M2N.13: 12 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, M.183, C.188, Y.194, G.225, V.226, L.229, P.230 Ligands: NAP.12 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.117, D:F.117, D:M.183, D:V.226, D:L.229 Hydrogen bonds: D:R.34, D:S.115, D:S.115, D:Y.194 Water bridges: D:R.34 pi-Stacking: D:F.117, D:F.117

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

ACT.3: 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.4: 5 residues within 4Å: Chain A: C.79, Q.80, S.92, E.95, I.96 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.95, A:I.96 ACT.7: 4 residues within 4Å: Chain A: K.278 Chain B: Q.206, G.274, I.276 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.206, B:I.276 Hydrogen bonds: B:Q.206 Water bridges: A:K.278, A:K.278, A:K.278 Salt bridges: A:K.278 ACT.10: 4 residues within 4Å: Chain C: Q.206, G.274, I.276 Chain D: K.278 8 PLIP interactions: 3 interactions with chain C, 5 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, D:K.278, D:K.278 Salt bridges: D:K.278 ACT.11: 3 residues within 4Å: Chain C: K.33, R.34, R.37 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.34 Salt bridges: C:R.37 ACT.14: 4 residues within 4Å: Chain C: K.278 Chain D: Q.206, G.274, I.276 8 PLIP interactions: 3 interactions with chain D, 5 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, C:K.278, C:K.278 Salt bridges: C:K.278

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khalaf, A.I. et al., Structure-Based Design and Synthesis of Antiparasitic Pyrrolopyrimidines Targeting Pteridine Reductase 1. J.Med.Chem. (2014)

Release Date

2015-01-21

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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