SMTL ID : 3h4v.2 (1 other biounit)

Selective screening and design to identify inhibitors of leishmania major pteridine reductase 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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.13, K.16, R.17, L.18, H.36, Y.37, H.38, R.39, S.40, A.64, D.65, L.66, S.67, N.109, A.110, S.111, S.112, D.142, S.146, M.179, V.180, D.181, K.198, P.224, G.225, L.226, S.227 Ligands: DVP.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.17, A:L.18, A:H.38, A:R.39, A:S.40, A:D.65, A:L.66, A:S.67, A:N.109, A:S.111, A:S.111, A:S.111, A:Y.194, A:K.198, A:S.227, A:S.227 Water bridges: A:G.13, A:K.16, A:H.38, A:H.38, A:S.40, A:N.109 Salt bridges: A:K.16, A:R.17, A:R.17 pi-Stacking: A:H.38 NAP.3: 27 residues within 4Å: Chain B: G.13, R.17, L.18, H.36, Y.37, H.38, R.39, S.40, A.64, D.65, L.66, S.67, N.109, A.110, S.111, S.112, D.142, M.179, V.180, D.181, Y.194, K.198, P.224, G.225, L.226, S.227 Ligands: DVP.4 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:P.224 Hydrogen bonds: B:R.17, B:L.18, B:H.38, B:R.39, B:S.40, B:D.65, B:D.65, B:L.66, B:S.67, B:N.109, B:S.111, B:S.111, B:S.111, B:K.198, B:S.227, B:S.227 Water bridges: B:A.15, B:A.15, B:G.19, B:N.109 Salt bridges: B:R.17, B:R.17 pi-Stacking: B:H.38 NAP.5: 26 residues within 4Å: Chain C: G.13, K.16, R.17, L.18, H.36, Y.37, H.38, R.39, S.40, A.64, D.65, L.66, S.67, N.109, S.111, S.112, D.142, M.179, V.180, D.181, Y.194, K.198, P.224, G.225, S.227 Ligands: DVP.6 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:L.18, C:H.38, C:R.39, C:S.40, C:L.66, C:S.67, C:N.109, C:S.111, C:S.111, C:S.111, C:D.142, C:Y.194, C:K.198, C:S.227, C:S.227 Water bridges: C:G.19, C:N.109 Salt bridges: C:R.17, C:R.17 pi-Stacking: C:H.38 NAP.7: 30 residues within 4Å: Chain D: G.13, A.15, K.16, R.17, L.18, H.36, Y.37, H.38, R.39, S.40, A.64, D.65, L.66, S.67, N.109, A.110, S.111, S.112, D.142, S.146, M.179, V.180, D.181, Y.194, K.198, P.224, G.225, L.226, S.227 Ligands: DVP.8 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:D.181, D:P.224 Hydrogen bonds: D:R.17, D:L.18, D:H.38, D:R.39, D:S.40, D:D.65, D:L.66, D:S.67, D:N.109, D:S.111, D:S.111, D:S.111, D:D.142, D:K.198, D:S.227, D:S.227 Water bridges: D:A.15, D:K.16, D:R.39 Salt bridges: D:K.16, D:R.17, D:R.17 pi-Stacking: D:H.38

4 x DVP: METHYL 1-(4-{[(2,4-DIAMINOPTERIDIN-6-YL)METHYL]AMINO}BENZOYL)PIPERIDINE-4-CARBOXYLATE(Non-covalent)

DVP.2: 12 residues within 4Å: Chain A: R.17, S.111, F.113, D.181, L.188, L.189, Y.191, Y.194, G.225, L.226, M.233 Ligands: NAP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.113, A:L.188, A:L.188, A:Y.191 Hydrogen bonds: A:R.17, A:S.111, A:S.111, A:Y.194 Water bridges: A:D.181, A:G.225 pi-Stacking: A:F.113, A:F.113 DVP.4: 11 residues within 4Å: Chain B: R.17, S.111, F.113, D.181, L.188, Y.191, Y.194, G.225, L.226, M.233 Ligands: NAP.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.113, B:L.188, B:Y.191 Hydrogen bonds: B:R.17, B:S.111 pi-Stacking: B:F.113, B:F.113 DVP.6: 8 residues within 4Å: Chain C: R.17, S.111, F.113, L.188, Y.194, G.225, L.226 Ligands: NAP.5 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.113, C:L.188 Hydrogen bonds: C:R.17, C:S.111, C:Y.194 Water bridges: C:R.17, C:G.225, B:R.287 pi-Stacking: C:F.113, C:F.113 DVP.8: 15 residues within 4Å: Chain D: R.17, S.111, S.112, F.113, P.115, D.181, L.188, Y.191, Y.194, G.225, L.226, L.229, D.232, H.241 Ligands: NAP.7 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.113, D:L.188, D:L.188, D:L.229 Hydrogen bonds: D:R.17, D:S.111, D:S.111 Water bridges: D:S.227 pi-Stacking: D:F.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cavazzuti, A. et al., Discovery of potent pteridine reductase inhibitors to guide antiparasite drug development. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2009-05-05

Peptides

Pteridine reductase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Pteridine reductase 1

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