SMTL ID : 2wd7.1

PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN COMPLEX WITH NADP AND DDD00066750

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: 28 residues within 4Å: Chain A: G.10, K.13, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: VGD.2 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:P.204 Hydrogen bonds: A:R.14, A:I.15, A:H.35, A:H.35, A:N.36, A:N.36, A:S.37, A:D.62, A:L.63, A:T.64, A:T.64, A:N.93, A:S.95, A:S.95, A:S.95, A:Y.174, A:K.178, A:S.207, A:L.208 Water bridges: A:K.13, A:R.14, A:G.16, A:S.37, A:S.37, A:N.93, A:S.95 Salt bridges: A:R.14, A:R.14 pi-Stacking: A:H.35 NAP.3: 27 residues within 4Å: Chain B: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: VGD.4 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:P.204 Hydrogen bonds: B:R.14, B:I.15, B:H.35, B:H.35, B:N.36, B:N.36, B:S.37, B:D.62, B:D.62, B:L.63, B:T.64, B:T.64, B:N.93, B:S.95, B:S.95, B:S.95, B:Y.174, B:K.178, B:S.207, B:L.208 Water bridges: B:G.16, B:S.37, B:S.37, B:N.93 Salt bridges: B:R.14, B:R.14 pi-Stacking: B:H.35 NAP.5: 27 residues within 4Å: Chain C: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: VGD.6 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:P.204 Hydrogen bonds: C:R.14, C:I.15, C:H.35, C:N.36, C:N.36, C:S.37, C:D.62, C:L.63, C:T.64, C:N.93, C:S.95, C:S.95, C:S.95, C:K.178, C:S.207, C:L.208 Water bridges: C:A.12, C:G.16, C:N.93, C:S.95 Salt bridges: C:R.14, C:R.14 pi-Stacking: C:H.35 NAP.7: 27 residues within 4Å: Chain D: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: VGD.8 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:P.204 Hydrogen bonds: D:R.14, D:I.15, D:H.35, D:N.36, D:N.36, D:S.37, D:D.62, D:D.62, D:L.63, D:T.64, D:N.93, D:S.95, D:S.95, D:S.95, D:K.178, D:G.205, D:S.207 Water bridges: D:G.10, D:G.16, D:N.93 Salt bridges: D:R.14, D:R.14 pi-Stacking: D:H.35

4 x VGD: 6-chloro-1H-benzimidazol-2-amine(Non-covalent)

VGD.2: 7 residues within 4Å: Chain A: S.95, F.97, D.161, Y.174, L.209, P.210 Ligands: NAP.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.95, A:S.95, A:Y.174 Water bridges: A:R.14, A:F.97 pi-Stacking: A:F.97, A:F.97 VGD.4: 6 residues within 4Å: Chain B: S.95, F.97, D.161, Y.174, P.210 Ligands: NAP.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.95, B:S.95, B:Y.174 pi-Stacking: B:F.97, B:F.97 VGD.6: 6 residues within 4Å: Chain C: S.95, F.97, D.161, Y.174, P.210 Ligands: NAP.5 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.95, C:S.95 Water bridges: C:R.14 pi-Stacking: C:F.97, C:F.97 VGD.8: 6 residues within 4Å: Chain D: S.95, F.97, D.161, Y.174, P.210 Ligands: NAP.7 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.95, D:S.95 Water bridges: D:R.14 pi-Stacking: D:F.97, D:F.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpamhanga, C.P. et al., One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening. J.Med.Chem. (2009)

Release Date

2009-06-30

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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