SMTL ID : 5l4n.1

Leishmania major Pteridine reductase 1 (PTR1) in complex with compound 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

2 x 6QT: (2~{R})-2-(3-hydroxyphenyl)-6-oxidanyl-2,3-dihydrochromen-4-one(Non-covalent)

6QT.1: 9 residues within 4Å: Chain A: R.17, S.111, F.113, L.188, Y.194, L.226, L.229 Chain D: R.287 Ligands: NDP.2 11 PLIP interactions: 2 interactions with chain D, 9 interactions with chain A Hydrogen bonds: D:R.287, D:R.287, A:R.17 Hydrophobic interactions: A:F.113, A:Y.194, A:L.226, A:L.229 Water bridges: A:D.181, A:D.181, A:D.181 pi-Stacking: A:F.113 6QT.4: 8 residues within 4Å: Chain B: R.17, S.111, F.113, L.188, Y.194, L.226 Chain C: R.287 Ligands: NDP.5 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.113, B:F.113, B:L.188, B:Y.194, B:L.226 Hydrogen bonds: B:R.17, C:R.287, C:R.287 Water bridges: B:S.111, B:F.113, B:D.181, B:D.181, B:D.181, B:G.225 pi-Stacking: B:F.113

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 29 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, Y.194, K.198, P.224, G.225, L.226, S.227 Ligands: 6QT.1 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:R.17, A:L.18, A:H.38, A:H.38, A:R.39, A:S.40, A:L.66, A:S.67, A:N.109, A:S.111, A:S.111, A:S.111, A:D.142, A:Y.194, A:K.198, A:S.227, A:S.227 Water bridges: A:G.13, A:R.17, A:G.19, A:N.109 Salt bridges: A:R.17, A:R.17 pi-Stacking: A:H.38 NDP.5: 28 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, S.146, M.179, V.180, D.181, Y.194, K.198, P.224, G.225, L.226, S.227 Ligands: 6QT.4 29 PLIP interactions: 29 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:L.66, B:S.67, B:N.109, B:S.111, B:S.111, B:S.111, B:D.142, B:D.142, B:K.198, B:S.227, B:S.227 Water bridges: B:G.13, B:A.15, B:S.40, B:S.40, B:N.109, B:N.109, B:S.112, B:S.112 Salt bridges: B:R.17, B:R.17 pi-Stacking: B:H.38 NDP.7: 27 residues within 4Å: Chain C: 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, S.146, M.179, V.180, D.181, Y.194, K.198, P.224, G.225, L.226, S.227 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:R.17, C:L.18, C:H.38, C:R.39, C:S.40, C:L.66, 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.13, C:A.15, C:G.19, C:H.38, C:H.38, C:S.40, C:S.40, C:S.67, C:N.109 Salt bridges: C:R.17, C:R.17 NDP.9: 28 residues within 4Å: Chain D: 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, Y.194, K.198, P.224, G.225, L.226, S.227 29 PLIP interactions: 29 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:S.112, D:S.112, D:K.198, D:S.227, D:S.227 Water bridges: D:G.13, D:A.15, D:A.15, D:K.16, D:G.19, D:S.40, D:N.109 Salt bridges: D:R.17, D:R.17 pi-Stacking: D:H.38

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Y.248, R.250 Chain C: Q.216, K.270 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.216, C:K.270, C:K.270, A:R.250

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

ACT.6: 2 residues within 4Å: Chain B: D.251, S.252 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.250

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 2 residues within 4Å: Chain C: Y.248, R.250 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.250

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10: 3 residues within 4Å: Chain B: K.270 Chain D: Y.248, R.250 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.248, D:R.250

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 3 residues within 4Å: Chain D: P.166, K.168, H.169 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.168, D:K.168 EDO.12: 4 residues within 4Å: Chain D: V.6, R.55, N.57, W.100 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.55 Water bridges: D:V.6 EDO.13: 3 residues within 4Å: Chain D: R.20, A.46, T.50 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.20, D:R.20, D:T.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Di Pisa, F. et al., Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity. Molecules (2017)

Release Date

2017-03-22

Peptides

Pteridine reductase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pteridine reductase 1

Related Entries With Identical Sequence