SMTL ID : 4cm8.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 27 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: IZ9.2 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: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:A.32, 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.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, 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: IZ9.6 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: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:A.32, B:G.36, B:S.57, B:S.57, 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: IZ9.9 27 PLIP interactions: 27 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:G.30, C:A.32, C:R.34, C:G.36, C:N.113, C:S.115, C:E.142 Salt bridges: C:R.34, C:R.34 pi-Stacking: C:H.55 NAP.12: 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, 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: IZ9.13 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:G.36, D:N.113, D:S.115 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

4 x IZ9: (E)-2,4-diamino-6-(4-methylstyryl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile(Non-covalent)

IZ9.2: 16 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, M.183, Q.186, C.188, Y.194, G.225, L.228, L.229, P.230, W.241 Chain D: H.287 Ligands: NAP.1, DTT.4 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:M.183, A:W.241, A:W.241, D:H.287 Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:D.181, A:D.181, A:Y.194 pi-Stacking: A:F.117, A:F.117 IZ9.6: 16 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, M.183, Q.186, C.188, Y.194, G.225, L.228, L.229, P.230, W.241 Chain C: H.287 Ligands: NAP.5, DTT.7 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:M.183, C:H.287 Hydrogen bonds: B:R.34, B:S.115, B:S.115, B:D.181, B:Y.194 Water bridges: B:R.34 pi-Stacking: B:F.117, B:F.117 IZ9.9: 16 residues within 4Å: Chain B: H.287 Chain C: R.34, S.115, F.117, D.181, M.183, Q.186, C.188, Y.194, G.225, L.228, L.229, P.230, W.241 Ligands: NAP.8, GOL.11 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:M.183, C:W.241, C:W.241, B:H.287 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 IZ9.13: 14 residues within 4Å: Chain A: H.287 Chain D: R.34, S.115, F.117, D.181, M.183, Q.186, C.188, Y.194, G.225, P.230, W.241 Ligands: NAP.12, GOL.14 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:M.183, D:W.241, D:W.241, A:H.287 Hydrogen bonds: D:R.34, D:S.115, D:S.115, D:Y.194 pi-Stacking: D:F.117, D:F.117

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

ACT.3: 3 residues within 4Å: Chain A: K.33, R.34, R.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.34 Salt bridges: A:R.37 ACT.10: 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

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

DTT.4: 8 residues within 4Å: Chain A: F.117, C.188, F.191, V.226, L.229, M.233, W.241 Ligands: IZ9.2 No protein-ligand interaction detected (PLIP) DTT.7: 7 residues within 4Å: Chain B: F.117, C.188, L.229, P.230, M.233, W.241 Ligands: IZ9.6 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.287

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 5 residues within 4Å: Chain C: F.117, C.188, M.233, W.241 Ligands: IZ9.9 No protein-ligand interaction detected (PLIP) GOL.14: 6 residues within 4Å: Chain D: F.117, C.188, V.226, M.233, W.241 Ligands: IZ9.13 No protein-ligand interaction detected (PLIP)

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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