SMTL ID : 5l42.1

Leishmania major Pteridine reductase 1 (PTR1) in complex with compound 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x 6J6: (2~{R})-2-[3,4-bis(oxidanyl)phenyl]-6-oxidanyl-2,3-dihydrochromen-4-one(Non-covalent)

6J6.1: 11 residues within 4Å: Chain A: R.17, S.111, F.113, L.188, Y.194, G.225, L.226, Y.283 Chain D: R.287 Ligands: NDP.2, ACT.7 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:R.287, A:S.111, A:Y.283 Water bridges: D:R.287, A:Y.283 Hydrophobic interactions: A:F.113, A:Y.194, A:L.226 pi-Stacking: A:F.113 6J6.11: 11 residues within 4Å: Chain B: R.17, S.111, F.113, L.188, Y.194, G.225, L.226, H.241, Y.283 Chain C: R.287 Ligands: NDP.12 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.113, B:L.188, B:Y.194, B:L.226 Hydrogen bonds: B:S.111, C:R.287 Water bridges: B:S.111, B:H.241, B:H.241, B:Y.283, B:Y.283 pi-Stacking: B:F.113 6J6.17: 13 residues within 4Å: Chain B: R.287 Chain C: R.17, S.111, F.113, M.183, L.188, Y.194, L.226, L.229, H.241 Ligands: NDP.18, GOL.19, EDO.20 18 PLIP interactions: 2 interactions with chain B, 16 interactions with chain C Hydrogen bonds: B:R.287, B:R.287, C:R.17, C:H.241, C:Y.283, C:Y.283 Hydrophobic interactions: C:F.113, C:L.188, C:Y.194, C:L.226, C:L.229 Water bridges: C:R.17, C:S.111, C:F.113, C:D.181, C:D.181, C:D.181 pi-Stacking: C:F.113 6J6.21: 13 residues within 4Å: Chain A: R.287 Chain D: R.17, S.111, F.113, M.183, L.188, Y.194, L.226, L.229, H.241, Y.283 Ligands: NDP.22, EDO.24 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:F.113, D:F.113, D:L.188, D:Y.194, D:L.226, D:L.229 Hydrogen bonds: D:R.17, D:S.111, D:H.241, D:Y.283, A:R.287, A:R.287 Water bridges: D:S.111, D:F.113, D:D.181, D:D.181, D:D.181 pi-Stacking: D:F.113

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

NDP.2: 30 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: 6J6.1, ACT.7 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:D.181, A:P.224 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:S.112, A:D.142, A:Y.194, A:K.198, A:S.227, A:S.227 Water bridges: A:G.13, A:A.15, A:K.16, A:K.16, A:K.16, A:K.16, A:G.19, A:N.109 Salt bridges: A:K.16, A:R.17, A:R.17 pi-Cation interactions: A:H.38 NDP.12: 28 residues within 4Å: Chain B: 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: 6J6.11, GOL.15 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:R.17, B:L.18, B:H.38, 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:G.13, B:G.19, B:S.40, B:S.40, B:N.109, B:S.112 Salt bridges: B:R.17, B:R.17 pi-Stacking: B:H.38 NDP.18: 29 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, 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: 6J6.17, GOL.19 28 PLIP interactions: 28 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: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.13, C:A.15, C:R.17, C:G.19, C:H.38, C:H.38, C:S.40, C:S.40, C:N.109 Salt bridges: C:R.17, C:R.17 pi-Stacking: C:H.38 NDP.22: 29 residues within 4Å: Chain D: 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: 6J6.21, EDO.24 27 PLIP interactions: 27 interactions with chain D Hydrogen bonds: D:R.17, D:L.18, D:H.38, D:H.38, D:R.39, D:S.40, D:D.65, D:D.65, D:L.66, D:S.67, D:N.109, D:S.111, D:S.111, D:S.111, D:K.198, D:S.227, D:S.227 Water bridges: D:G.13, D:A.15, D:K.16, D:G.19, D:S.40, D:N.109, D:S.112 Salt bridges: D:R.17, D:R.17 pi-Cation interactions: D:H.38

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Y.97, R.161, G.164, T.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.161, A:R.161, A:R.161 GOL.4: 4 residues within 4Å: Chain A: Q.216, K.270 Chain C: Y.248, R.250 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.250, A:Q.216 GOL.13: 4 residues within 4Å: Chain B: Q.216, K.270 Chain D: Y.248, R.250 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.216, B:K.270, D:R.250 GOL.14: 6 residues within 4Å: Chain B: V.228, R.242, R.250, D.251, S.252, S.253 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.242, B:D.251 GOL.15: 1 residues within 4Å: Ligands: NDP.12 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.16, B:S.111, B:F.113 GOL.19: 5 residues within 4Å: Chain C: R.17, F.113, V.230 Ligands: 6J6.17, NDP.18 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.17, C:R.17, C:F.113, C:F.113

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

ACT.5: 3 residues within 4Å: Chain A: H.99, W.100, G.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.100 ACT.6: 3 residues within 4Å: Chain A: R.20, A.46, T.50 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.50 Water bridges: A:L.47, A:T.50 Salt bridges: A:R.20 ACT.7: 4 residues within 4Å: Chain A: R.17, V.230 Ligands: 6J6.1, NDP.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.230 Water bridges: A:V.228 Salt bridges: A:R.17 ACT.16: 3 residues within 4Å: Chain B: Y.248, R.250 Chain D: Q.216 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Salt bridges: B:R.250 Hydrogen bonds: D:Q.216

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

PGE.8: 5 residues within 4Å: Chain A: Y.248, R.250 Chain C: T.172, Q.216, K.270 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.216, C:K.270, A:R.250

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

EDO.9: 2 residues within 4Å: Chain A: P.166, K.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.168, A:K.168 EDO.10: 5 residues within 4Å: Chain A: V.6, P.56, N.57, S.58, W.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.55 EDO.20: 4 residues within 4Å: Chain C: F.113, L.188, Y.191 Ligands: 6J6.17 No protein-ligand interaction detected (PLIP) EDO.23: 2 residues within 4Å: Chain D: P.166, H.169 No protein-ligand interaction detected (PLIP) EDO.24: 3 residues within 4Å: Chain D: R.17 Ligands: 6J6.21, NDP.22 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.17

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

2017-05-03

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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